4FBY

fs X-ray diffraction of Photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.56 Å
  • R-Value Free: 0.385 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.367 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Kern, J.Alonso-Mori, R.Hellmich, J.Tran, R.Hattne, J.Laksmono, H.Glockner, C.Echols, N.Sierra, R.G.Sellberg, J.Lassalle-Kaiser, B.Gildea, R.J.Glatzel, P.Grosse-Kunstleve, R.W.Latimer, M.J.McQueen, T.A.DiFiore, D.Fry, A.R.Messerschmidt, M.Miahnahri, A.Schafer, D.W.Seibert, M.M.Sokaras, D.Weng, T.C.Zwart, P.H.White, W.E.Adams, P.D.Bogan, M.J.Boutet, S.Williams, G.J.Messinger, J.Sauter, N.K.Zouni, A.Bergmann, U.Yano, J.Yachandra, V.K.

(2012) Proc Natl Acad Sci U S A 109: 9721-9726

  • DOI: https://doi.org/10.1073/pnas.1204598109
  • Primary Citation of Related Structures:  
    4FBY

  • PubMed Abstract: 

    Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
U [auth G]
344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth N]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth P]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth Q]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth R]
83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth S]
44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth W],
G [auth H]
65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth a],
H [auth I]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth b],
I [auth J]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth c],
J [auth K]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth d],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth e],
L [auth M]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth f],
M [auth O]
246Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth g],
N [auth T]
32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth h],
O [auth U]
104Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth i],
P [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ycf12KA [auth m],
Q [auth y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth j],
R [auth X]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein YMA [auth k],
S [auth Y]
28Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth l],
T [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DC [auth B]
DH [auth W]
HG [auth P]
IG [auth P]
JD [auth D]
DC [auth B],
DH [auth W],
HG [auth P],
IG [auth P],
JD [auth D],
LE [auth G],
LG [auth P],
TC [auth C],
UA [auth A],
UE [auth N],
UG [auth Q],
VC [auth C],
WB [auth B],
XC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AF [auth N]
AG [auth P]
BF [auth N]
BG [auth P]
CB [auth B]
AF [auth N],
AG [auth P],
BF [auth N],
BG [auth P],
CB [auth B],
CD [auth D],
CF [auth N],
CG [auth P],
DB [auth B],
DF [auth N],
EB [auth B],
EF [auth N],
EG [auth P],
FB [auth B],
FD [auth D],
FE [auth G],
FF [auth N],
GB [auth B],
GC [auth C],
GE [auth G],
GF [auth N],
GG [auth P],
HB [auth B],
HC [auth C],
HF [auth N],
IB [auth B],
IC [auth C],
IE [auth G],
IF [auth N],
JB [auth B],
JC [auth C],
JF [auth N],
KB [auth B],
KC [auth C],
KE [auth G],
LB [auth B],
LC [auth C],
LF [auth N],
MB [auth B],
MC [auth C],
MF [auth N],
NB [auth B],
NC [auth C],
OA [auth A],
OB [auth B],
OC [auth C],
OF [auth N],
PA [auth A],
PB [auth B],
QA [auth A],
QB [auth B],
QC [auth C],
QG [auth Q],
RB [auth B],
SA [auth A],
SC [auth C],
SF [auth P],
SG [auth Q],
TF [auth P],
UC [auth C],
UF [auth P],
VF [auth P],
WC [auth C],
WF [auth P],
XE [auth N],
XF [auth P],
YE [auth N],
YF [auth P],
ZE [auth N],
ZF [auth P]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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AD [auth D],
HE [auth G],
NG [auth Q],
RA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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BB [auth A]
BH [auth S]
CC [auth B]
EE [auth G]
ME [auth G]
BB [auth A],
BH [auth S],
CC [auth B],
EE [auth G],
ME [auth G],
OD [auth F],
TE [auth N],
TG [auth Q],
WA [auth A],
ZB [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
LMG
Query on LMG

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DD [auth D]
ED [auth D]
FH [auth a]
KG [auth P]
LD [auth D]
DD [auth D],
ED [auth D],
FH [auth a],
KG [auth P],
LD [auth D],
LH [auth e],
MG [auth P],
ND [auth E],
NF [auth N],
OE [auth G],
OG [auth Q],
QF [auth N],
RD [auth I],
RG [auth Q],
VG [auth Q],
WD [auth M],
XA [auth A],
XB [auth B],
YB [auth B],
YC [auth C],
ZC [auth C],
ZG [auth R]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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BD [auth D]
HH [auth b]
JE [auth G]
PG [auth Q]
TA [auth A]
BD [auth D],
HH [auth b],
JE [auth G],
PG [auth Q],
TA [auth A],
TD [auth J]
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
LHG
Query on LHG

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NE [auth G],
PE [auth G],
VA [auth A],
YA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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CE [auth V],
MD [auth E],
NH [auth i],
YG [auth R]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AE [auth T]
AH [auth S]
BE [auth T]
CH [auth W]
DE [auth Z]
AE [auth T],
AH [auth S],
BE [auth T],
CH [auth W],
DE [auth Z],
DG [auth P],
EH [auth a],
FG [auth P],
GD [auth D],
IH [auth b],
JG [auth P],
JH [auth c],
KF [auth N],
PC [auth C],
PD [auth H],
QD [auth I],
RC [auth C],
SB [auth B],
TB [auth B],
UB [auth B],
UD [auth J],
VB [auth B],
VD [auth K],
ZD [auth T]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AC [auth B]
BC [auth B]
EC [auth B]
FC [auth B]
GH [auth a]
AC [auth B],
BC [auth B],
EC [auth B],
FC [auth B],
GH [auth a],
KD [auth D],
KH [auth e],
PF [auth N],
RF [auth N],
SD [auth I],
VE [auth N],
WE [auth N],
WG [auth Q],
XD [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC
Query on OEC

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QE [auth G],
ZA [auth A]
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
BCT
Query on BCT

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HD [auth D],
XG [auth Q]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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AB [auth A],
RE [auth G]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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MH [auth f],
YD [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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ID [auth D],
SE [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.56 Å
  • R-Value Free: 0.385 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.367 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.783α = 90
b = 227.764β = 90
c = 308.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Non-polymer description
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Data collection
  • Version 1.4: 2017-11-15
    Changes: Data collection
  • Version 1.5: 2017-11-29
    Changes: Database references
  • Version 1.6: 2018-02-14
    Changes: Data collection
  • Version 2.0: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description