4TNH

RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G., Gildea, R.J., Han, G., Hellmich, J., Lassalle-Kaiser, B., Chatterjee, R., Brewster, A.S., Stan, C.A., Glockner, C., Lampe, A., DiFiore, D., Milathianaki, D., Fry, A.R., Seibert, M.M., Koglin, J.E., Gallo, E., Uhlig, J., Sokaras, D., Weng, T.C., Zwart, P.H., Skinner, D.E., Bogan, M.J., Messerschmidt, M., Glatzel, P., Williams, G.J., Boutet, S., Adams, P.D., Zouni, A., Messinger, J., Sauter, N.K., Bergmann, U., Yano, J., Yachandra, V.K.

(2014) Nat Commun 5: 4371-4371

  • DOI: https://doi.org/10.1038/ncomms5371
  • Primary Citation of Related Structures:  
    4TNH, 4TNI, 4TNJ, 4TNK, 4TNL

  • PubMed Abstract: 

    • The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser ...

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213
    Organizational Affiliation: 

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
U [auth a]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1, psbA-1, tlr1843
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A444 
Go to UniProtKB:  P0A444
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A444
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbB, tlr1530
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIQ1 
Go to UniProtKB:  Q8DIQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIQ1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbC, tlr1631
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIF8 
Go to UniProtKB:  Q8DIF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIF8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1, tlr0455, psbD2, tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8CM25 
Go to UniProtKB:  Q8CM25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CM25
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbE, tsr1541
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIP0 
Go to UniProtKB:  Q8DIP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIP0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbF, tsr1542
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIN9 
Go to UniProtKB:  Q8DIN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIN9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbH, tsl1386
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJ43 
Go to UniProtKB:  Q8DJ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJ43
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbI, tsr1074
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJZ6 
Go to UniProtKB:  Q8DJZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJZ6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbJ, tsr1544
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P59087 
Go to UniProtKB:  P59087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59087
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbK, tsl0176
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1K9 
Go to UniProtKB:  Q9F1K9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1K9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbL, tsr1543
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIN8 
Go to UniProtKB:  Q8DIN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIN8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbM, tsl2052
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DHA7 
Go to UniProtKB:  Q8DHA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DHA7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbO, tll0444
Membrane Entity: Yes 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A431 
Go to UniProtKB:  P0A431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A431
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbT, tsr1531
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIQ0 
Go to UniProtKB:  Q8DIQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIQ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbU, tll2409
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1L5 
Go to UniProtKB:  Q9F1L5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1L5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbV, tll1285
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A386 
Go to UniProtKB:  P0A386
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A386
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth g],
Q [auth y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12, tsr1242
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJI1 
Go to UniProtKB:  Q8DJI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJI1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth x],
R [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbX, tsr2013
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1R6 
Go to UniProtKB:  Q9F1R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1R6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein YMA [auth G],
S [auth Y]		28Thermosynechococcus vestitus BP-1Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth z],
T [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZ, tsr1967
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DHJ2 
Go to UniProtKB:  Q8DHJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DHJ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
Download Ideal Coordinates CCD File 
BC [auth B]
HG [auth c]
ID [auth D]
IG [auth c]
JG [auth c]
BC [auth B],
HG [auth c],
ID [auth D],
IG [auth c],
JG [auth c],
NE [auth a],
PF [auth b],
SE [auth b],
TC [auth C],
UC [auth C],
VA [auth A],
VC [auth C],
WB [auth B],
XG [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N		 Ligand Interaction
CLA
Query on CLA
Download Ideal Coordinates CCD File 
AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CF [auth b]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CF [auth b],
CG [auth c],
DB [auth B],
DD [auth D],
DF [auth b],
DG [auth c],
EB [auth B],
ED [auth D],
EF [auth b],
EG [auth c],
EH [auth h],
FB [auth B],
FC [auth C],
FF [auth b],
GB [auth B],
GC [auth C],
GE [auth a],
GF [auth b],
HB [auth B],
HC [auth C],
HE [auth a],
HF [auth b],
IB [auth B],
IC [auth C],
IE [auth a],
IF [auth b],
JB [auth B],
JC [auth C],
JF [auth b],
KB [auth B],
KC [auth C],
KE [auth a],
KF [auth b],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
MG [auth c],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PA [auth A],
PB [auth B],
PC [auth C],
PD [auth H],
QA [auth A],
QB [auth B],
QC [auth C],
RA [auth A],
RB [auth B],
SA [auth A],
SG [auth d],
TF [auth c],
TG [auth d],
UF [auth c],
VF [auth c],
WE [auth b],
WF [auth c],
XE [auth b],
XF [auth c],
YC [auth C],
YE [auth b],
YF [auth c],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M		 Ligand Interaction
PHO
Query on PHO
Download Ideal Coordinates CCD File 
AD [auth D],
BD [auth D],
JE [auth a],
PG [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N		 Ligand Interaction
SQD
Query on SQD
Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CC [auth B]
DE [auth a]
DH [auth f]
AB [auth A],
BB [auth A],
CC [auth B],
DE [auth a],
DH [auth f],
OD [auth F],
QG [auth d],
RE [auth a],
TE [auth b],
YB [auth B]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N		 Ligand Interaction
LMG
Query on LMG
Download Ideal Coordinates CCD File 
AH [auth e]
CB [auth A]
EE [auth a]
FH [auth i]
GD [auth D]
AH [auth e],
CB [auth A],
EE [auth a],
FH [auth i],
GD [auth D],
HD [auth D],
KD [auth D],
KG [auth c],
KH [auth l],
LD [auth E],
LH [auth m],
OG [auth c],
QF [auth b],
RD [auth I],
VG [auth d],
WC [auth C],
WG [auth d],
XA [auth A],
XB [auth B],
XD [auth M],
ZC [auth C],
ZG [auth d]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
PL9
Query on PL9
Download Ideal Coordinates CCD File 
FD [auth D]
HH [auth j]
LE [auth a]
TA [auth A]
TD [auth J]
FD [auth D],
HH [auth j],
LE [auth a],
TA [auth A],
TD [auth J],
UG [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N		 Ligand Interaction
LHG
Query on LHG
Download Ideal Coordinates CCD File 
LG [auth c],
OE [auth a],
WA [auth A],
XC [auth C]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
BE [auth V],
BH [auth f],
MD [auth F],
NH [auth v]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
BCR
Query on BCR
Download Ideal Coordinates CCD File 
CE [auth y]
CH [auth f]
FG [auth c]
GG [auth c]
IH [auth j]
CE [auth y],
CH [auth f],
FG [auth c],
GG [auth c],
IH [auth j],
LF [auth b],
ME [auth a],
MF [auth b],
ND [auth F],
NF [auth b],
NG [auth c],
OF [auth b],
OH [auth g],
PH [auth x],
QD [auth H],
RC [auth C],
SB [auth B],
SC [auth C],
TB [auth B],
UA [auth A],
UB [auth B],
UD [auth J],
VB [auth B],
WD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
LMT
Query on LMT
Download Ideal Coordinates CCD File 
AC [auth B]
DC [auth B]
EC [auth B]
GH [auth i]
JD [auth D]
AC [auth B],
DC [auth B],
EC [auth B],
GH [auth i],
JD [auth D],
RF [auth b],
SD [auth I],
SF [auth b],
UE [auth b],
VE [auth b],
YD [auth M],
YG [auth d],
ZB [auth B],
ZD [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
OEX
Query on OEX
Download Ideal Coordinates CCD File 
QE [auth a],
ZA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N		 Ligand Interaction
BCT
Query on BCT
Download Ideal Coordinates CCD File 
CD [auth D],
RG [auth d]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
FE [auth a],
OA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
AE [auth O],
JH [auth k],
MH [auth o],
VD [auth K]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
PE [auth a],
YA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.885α = 90
b = 229.033β = 90
c = 307.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095887
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102520
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2015-10-07
    Changes: Other
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description