5B5E

Crystal structure analysis of Photosystem II complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 2.1 of the entry. See complete history. 


Literature

Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II

Tanaka, A., Fukushima, Y., Kamiya, N.

(2017) J Am Chem Soc 139: 1718-1721

  • DOI: https://doi.org/10.1021/jacs.6b09666
  • Primary Citation of Related Structures:  
    5B5E, 5B66

  • PubMed Abstract: 

    • The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies ...

    The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S 0 -state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S 1 -state of the Kok cycle should be re-evaluated.

    Organizational Affiliation: 

    The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1A,
T [auth a]		344Thermostichus vulcanusMutation(s): 0 
Gene Names: psbA, psbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]		505Thermostichus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]		455Thermostichus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		342Thermostichus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		83Thermostichus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		44Thermostichus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]		65Thermostichus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]		40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
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Find proteins for Q7DGD4 (Thermostichus vulcanus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
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Find proteins for P12312 (Thermostichus vulcanus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
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Find proteins for P0A387 (Thermostichus vulcanus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Gene Names: ycf12, psbY
Membrane Entity: Yes 
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Find proteins for D0VWR3 (Thermostichus vulcanus)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus)
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Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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OF [auth H]
QM [auth h]
UE [auth D]
WK [auth c]
XD [auth C]
OF [auth H],
QM [auth h],
UE [auth D],
WK [auth c],
XD [auth C],
XK [auth c],
XL [auth d],
YD [auth C],
YK [auth c],
ZD [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N		 Ligand Interaction
CLA
Query on CLA
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AC [auth B]
AJ [auth b]
BJ [auth b]
HK [auth c]
ID [auth C]
AC [auth B],
AJ [auth b],
BJ [auth b],
HK [auth c],
ID [auth C],
IK [auth c],
JD [auth C],
JK [auth c],
KD [auth C],
KK [auth c],
LB [auth B],
LD [auth C],
LK [auth c],
MB [auth B],
MD [auth C],
MI [auth b],
MK [auth c],
NB [auth B],
ND [auth C],
NI [auth b],
NK [auth c],
OB [auth B],
OD [auth C],
OE [auth D],
OI [auth b],
OK [auth c],
PB [auth B],
PD [auth C],
PI [auth b],
PK [auth c],
QA [auth A],
QB [auth B],
QD [auth C],
QE [auth D],
QI [auth b],
QK [auth c],
RA [auth A],
RB [auth B],
RD [auth C],
RE [auth D],
RI [auth b],
RK [auth c],
RL [auth d],
SB [auth B],
SD [auth C],
SH [auth a],
SI [auth b],
SK [auth c],
TA [auth A],
TB [auth B],
TD [auth C],
TH [auth a],
TI [auth b],
TK [auth c],
TL [auth d],
UB [auth B],
UD [auth C],
UI [auth b],
UL [auth d],
VB [auth B],
VI [auth b],
WB [auth B],
WH [auth a],
WI [auth b],
XB [auth B],
XI [auth b],
YB [auth B],
YI [auth b],
ZB [auth B],
ZI [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M		 Ligand Interaction
PHO
Query on PHO
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PE [auth D],
SA [auth A],
UH [auth a],
VH [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N		 Ligand Interaction
SQD
Query on SQD
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AB [auth A]
CG [auth L]
DI [auth a]
EC [auth B]
JO [auth x]
AB [auth A],
CG [auth L],
DI [auth a],
EC [auth B],
JO [auth x],
VA [auth A],
VE [auth D],
YH [auth a]
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
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AE [auth C]
AN [auth j]
BM [auth d]
FC [auth B]
HD [auth C]
AE [auth C],
AN [auth j],
BM [auth d],
FC [auth B],
HD [auth C],
JL [auth c],
KN [auth m],
LE [auth C],
VF [auth J],
ZE [auth D],
ZH [auth a],
ZK [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
PL9
Query on PL9
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AI [auth a],
TE [auth D],
WA [auth A],
WL [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
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AG [auth K]
AM [auth d]
BG [auth L]
BI [auth a]
FF [auth E]
AG [auth K],
AM [auth d],
BG [auth L],
BI [auth a],
FF [auth E],
HN [auth l],
KM [auth e],
SL [auth d],
WE [auth D],
XA [auth A],
XE [auth D],
YE [auth D],
YL [auth d],
ZL [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N		 Ligand Interaction
HEC
Query on HEC
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BO [auth v],
ZG [auth V]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
HEM
Query on HEM
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JF [auth E],
OM [auth e]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
RRX
Query on RRX
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KO [auth x],
NF [auth H]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N		 Ligand Interaction
BCR
Query on BCR
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BC [auth B]
CC [auth B]
CJ [auth b]
DC [auth B]
DJ [auth b]
BC [auth B],
CC [auth B],
CJ [auth b],
DC [auth B],
DJ [auth b],
DN [auth j],
EJ [auth b],
FN [auth k],
IH [auth Y],
KE [auth C],
QG [auth T],
RN [auth t],
SE [auth D],
UA [auth A],
UK [auth c],
VD [auth C],
VK [auth c],
VL [auth d],
WD [auth C],
XH [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
LMT
Query on LMT
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AD [auth B]
BB [auth A]
BD [auth B]
DG [auth M]
EI [auth a]
AD [auth B],
BB [auth A],
BD [auth B],
DG [auth M],
EI [auth a],
FJ [auth b],
GC [auth B],
II [auth a],
KF [auth F],
KH [auth Z],
LN [auth m],
MM [auth e],
MN [auth m],
MO [auth z],
RF [auth I],
SG [auth T]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
OEX
Query on OEX
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MA [auth A],
OH [auth a]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N		 Ligand Interaction
HTG
Query on HTG
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AH [auth V]
AL [auth c]
BE [auth C]
BF [auth D]
BL [auth c]
AH [auth V],
AL [auth c],
BE [auth C],
BF [auth D],
BL [auth c],
CE [auth C],
CL [auth c],
CO [auth v],
DE [auth C],
DM [auth d],
GG [auth O],
GJ [auth b],
HC [auth B],
HJ [auth b],
IC [auth B],
JC [auth B],
LJ [auth b],
MJ [auth b],
NC [auth B],
OC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N		 Ligand Interaction
DMS
Query on DMS
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AK [auth b]
AO [auth v]
BH [auth V]
BK [auth b]
CD [auth B]
AK [auth b],
AO [auth v],
BH [auth V],
BK [auth b],
CD [auth B],
CF [auth D],
CH [auth V],
CK [auth b],
DB [auth A],
DD [auth B],
DF [auth D],
DH [auth V],
DK [auth b],
DL [auth c],
DO [auth v],
EB [auth A],
ED [auth B],
EE [auth C],
EF [auth D],
EH [auth V],
EK [auth b],
EL [auth c],
EM [auth d],
EO [auth v],
FD [auth B],
FE [auth C],
FH [auth V],
FK [auth b],
FL [auth c],
FM [auth d],
FO [auth v],
GB [auth A],
GD [auth B],
GE [auth C],
GH [auth V],
GI [auth a],
GL [auth c],
GM [auth d],
GN [auth k],
GO [auth v],
HB [auth A],
HE [auth C],
HG [auth O],
HH [auth V],
HI [auth a],
HL [auth c],
HO [auth v],
IB [auth A],
IE [auth C],
IG [auth O],
IL [auth c],
IM [auth d],
IN [auth l],
IO [auth v],
JB [auth A],
JE [auth C],
JG [auth O],
JI [auth a],
JM [auth d],
KG [auth O],
LF [auth F],
LG [auth O],
LL [auth c],
MF [auth H],
MG [auth O],
ML [auth c],
NE [auth C],
NG [auth O],
NH [auth a],
NL [auth c],
NM [auth e],
NN [auth o],
OG [auth O],
OL [auth c],
PG [auth O],
PL [auth c],
PM [auth h],
PN [auth o],
QF [auth H],
QL [auth c],
QN [auth o],
RJ [auth b],
RM [auth h],
SJ [auth b],
SM [auth h],
TC [auth B],
TJ [auth b],
TM [auth h],
UC [auth B],
UG [auth U],
UJ [auth b],
VC [auth B],
VG [auth U],
VJ [auth b],
VN [auth u],
WC [auth B],
WG [auth U],
WJ [auth b],
WN [auth u],
XC [auth B],
XG [auth V],
XJ [auth b],
XN [auth u],
YC [auth B],
YG [auth V],
YJ [auth b],
YM [auth i],
YN [auth u],
ZC [auth B],
ZJ [auth b],
ZM [auth i],
ZN [auth v]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
BCT
Query on BCT
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FB [auth A],
KI [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
FE2
Query on FE2
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NA [auth A],
PH [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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FG [auth O],
GK [auth c],
KB [auth B],
LI [auth b],
ON [auth o]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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OA [auth A],
PA [auth A],
QH [auth a],
RH [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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BN [auth j],
WF [auth J]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
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AF [auth D]
CB [auth A]
CI [auth a]
CM [auth d]
CN [auth j]
AF [auth D],
CB [auth A],
CI [auth a],
CM [auth d],
CN [auth j],
EG [auth M],
EN [auth k],
FI [auth a],
GF [auth E],
HF [auth E],
HM [auth d],
IF [auth E],
IJ [auth b],
JH [auth X],
JJ [auth b],
JN [auth m],
KC [auth B],
KJ [auth b],
KL [auth c],
LC [auth B],
LH [auth Z],
LM [auth e],
LO [auth x],
MC [auth B],
ME [auth C],
MH [auth Z],
NJ [auth b],
NO [auth z],
OJ [auth b],
PC [auth B],
PF [auth H],
PJ [auth b],
QC [auth B],
QJ [auth b],
RC [auth B],
RG [auth T],
SC [auth B],
SF [auth I],
SN [auth t],
TF [auth I],
TG [auth U],
TN [auth u],
UF [auth I],
UM [auth i],
UN [auth u],
VM [auth i],
WM [auth i],
XF [auth J],
XM [auth i],
YA [auth A],
YF [auth J],
ZA [auth A],
ZF [auth J]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME		AA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.404α = 90
b = 228.224β = 90
c = 286.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

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
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 2.0: 2019-10-09
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary