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 5B66 | pdb_00005b66

Crystal structure analysis of Photosystem II complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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This is version 4.0 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 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. 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: 
    • Department of Chemistry, Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.

Macromolecule Content 

  • Total Structure Weight: 744.34 kDa 
  • Atom Count: 54,996 
  • Modeled Residue Count: 5,234 
  • Deposited Residue Count: 5,350 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
T [auth a]		344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Find proteins for P51765 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]		505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0VWR1 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]		455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0VWR7 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12238 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]		65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P19052 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P12240 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q7DGD4 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P19054 (Thermostichus vulcanus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P12312 (Thermostichus vulcanus)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0VWR2 (Thermostichus vulcanus)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P12313 (Thermostichus vulcanus)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P56152 (Thermostichus vulcanus)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P0A387 (Thermostichus vulcanus)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0VWR3 (Thermostichus vulcanus)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for D0VWR5 (Thermostichus vulcanus)
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Reference Sequence

Small Molecules

Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
AM [auth h]
IF [auth H]
KK [auth c]
LK [auth c]
MK [auth c]
AM [auth h],
IF [auth H],
KK [auth c],
LK [auth c],
MK [auth c],
PE [auth D],
RD [auth C],
SD [auth C],
TD [auth C],
VL [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AK [auth c]
BK [auth c]
CD [auth C]
CK [auth c]
DD [auth C]
AK [auth c],
BK [auth c],
CD [auth C],
CK [auth c],
DD [auth C],
DK [auth c],
ED [auth C],
EI [auth b],
EK [auth c],
FD [auth C],
FI [auth b],
FK [auth c],
GD [auth C],
GI [auth b],
GK [auth c],
HB [auth B],
HD [auth C],
HI [auth b],
HK [auth c],
HL [auth d],
IB [auth B],
ID [auth C],
II [auth b],
IK [auth c],
IL [auth d],
JB [auth B],
JD [auth C],
JI [auth b],
JL [auth d],
KB [auth B],
KD [auth C],
KE [auth D],
KI [auth b],
LB [auth B],
LD [auth C],
LE [auth D],
LH [auth a],
LI [auth b],
MA [auth A],
MB [auth B],
MD [auth C],
MH [auth a],
MI [auth b],
NA [auth A],
NB [auth B],
ND [auth C],
NE [auth D],
NI [auth b],
OB [auth B],
OD [auth C],
OI [auth b],
PA [auth A],
PB [auth B],
PH [auth a],
PI [auth b],
QB [auth B],
QI [auth b],
RB [auth B],
RI [auth b],
SB [auth B],
SI [auth b],
TB [auth B],
TI [auth b],
UB [auth B],
VB [auth B],
WB [auth B],
WJ [auth c],
XJ [auth c],
YJ [auth c],
ZJ [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


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ME [auth D],
NH [auth a],
OA [auth A],
OH [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
FF [auth F]
JH [auth a]
PM [auth l]
RA [auth A]
RH [auth a]
FF [auth F],
JH [auth a],
PM [auth l],
RA [auth A],
RH [auth a],
XA [auth A],
XI [auth b],
YL [auth f]
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


Download:Ideal Coordinates CCD File
AC [auth B]
HM [auth j]
NK [auth c]
OK [auth c]
SA [auth A]
AC [auth B],
HM [auth j],
NK [auth c],
OK [auth c],
SA [auth A],
SF [auth J],
SH [auth a],
UD [auth C],
YI [auth b],
ZD [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


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RL [auth d],
VE [auth D],
WA [auth A],
XH [auth a]		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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BG [auth L]
DF [auth E]
LL [auth d]
ML [auth d]
NL [auth d]
BG [auth L],
DF [auth E],
LL [auth d],
ML [auth d],
NL [auth d],
QE [auth D],
QM [auth l],
RE [auth D],
SE [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC


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HN [auth v],
XG [auth V]		HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM


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EF [auth E],
XL [auth e]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX


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HF [auth H],
RN [auth x]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR


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AG [auth K]
BN [auth t]
IM [auth j]
JK [auth c]
KL [auth d]
AG [auth K],
BN [auth t],
IM [auth j],
JK [auth c],
KL [auth d],
NM [auth k],
OE [auth D],
OM [auth k],
PD [auth C],
QA [auth A],
QD [auth C],
QG [auth T],
QH [auth a],
UI [auth b],
VI [auth b],
WI [auth b],
XB [auth B],
YB [auth B],
ZB [auth B],
ZF [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


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AI [auth a]
BF [auth E]
CJ [auth b]
DG [auth M]
DJ [auth b]
AI [auth a],
BF [auth E],
CJ [auth b],
DG [auth M],
DJ [auth b],
FC [auth B],
GC [auth B],
HC [auth B],
HH [auth Z],
MF [auth I],
RG [auth T],
RM [auth m],
SK [auth c],
SM [auth m],
UF [auth J],
UN [auth z],
ZL [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX


Download:Ideal Coordinates CCD File
BI [auth a],
FB [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG

Query on HTG


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AF [auth D]
AJ [auth b]
BC [auth B]
CC [auth B]
CI [auth b]
AF [auth D],
AJ [auth b],
BC [auth B],
CC [auth B],
CI [auth b],
DC [auth B],
DI [auth b],
DN [auth u],
GG [auth O],
GL [auth d],
JE [auth C],
LC [auth B],
MC [auth B],
PK [auth c],
QK [auth c],
QN [auth v],
VD [auth C],
WD [auth C],
XD [auth C],
YG [auth V],
ZI [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
DMS

Query on DMS


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AB [auth A]
AE [auth C]
AH [auth V]
AL [auth c]
AN [auth o]
AB [auth A],
AE [auth C],
AH [auth V],
AL [auth c],
AN [auth o],
BB [auth A],
BE [auth C],
BH [auth V],
BL [auth c],
BM [auth h],
CB [auth A],
CE [auth C],
CH [auth V],
CL [auth c],
DB [auth A],
DE [auth C],
DH [auth V],
DL [auth c],
EE [auth C],
EH [auth V],
EL [auth c],
EN [auth u],
FE [auth C],
FH [auth V],
FL [auth c],
FN [auth u],
GE [auth C],
GF [auth F],
GJ [auth b],
GM [auth i],
GN [auth u],
HE [auth C],
HG [auth O],
HJ [auth b],
IE [auth C],
IG [auth O],
IJ [auth b],
IN [auth v],
JF [auth H],
JG [auth O],
JJ [auth b],
JN [auth v],
KG [auth O],
KJ [auth b],
KN [auth v],
LG [auth O],
LJ [auth b],
LM [auth j],
LN [auth v],
MG [auth O],
MJ [auth b],
MN [auth v],
NG [auth O],
NJ [auth b],
NN [auth v],
OC [auth B],
OG [auth O],
OJ [auth b],
ON [auth v],
PC [auth B],
PG [auth O],
PJ [auth b],
PN [auth v],
QC [auth B],
QJ [auth b],
RC [auth B],
SC [auth B],
SL [auth d],
TC [auth B],
TL [auth d],
UC [auth B],
UG [auth U],
UL [auth d],
UM [auth o],
VC [auth B],
VG [auth U],
VM [auth o],
WC [auth B],
WE [auth D],
WG [auth U],
WK [auth c],
WM [auth o],
XC [auth B],
XE [auth D],
XK [auth c],
XM [auth o],
YC [auth B],
YE [auth D],
YK [auth c],
YM [auth o],
ZA [auth A],
ZC [auth B],
ZE [auth D],
ZK [auth c],
ZM [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
GB [auth A],
VH [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
EB [auth A],
ZH [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
BJ [auth b]
EC [auth B]
FG [auth O]
RK [auth c]
TM [auth o]
BJ [auth b],
EC [auth B],
FG [auth O],
RK [auth c],
TM [auth o],
ZG [auth V]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
TA [auth A],
TH [auth a],
UA [auth A],
UH [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
JM [auth j],
TF [auth J]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
AD [auth B]
BD [auth B]
CF [auth E]
CG [auth L]
CM [auth h]
AD [auth B],
BD [auth B],
CF [auth E],
CG [auth L],
CM [auth h],
CN [auth t],
DM [auth i],
EG [auth M],
EJ [auth b],
EM [auth i],
FJ [auth b],
FM [auth i],
GH [auth X],
IC [auth B],
IH [auth Z],
JC [auth B],
KC [auth B],
KF [auth H],
KH [auth a],
KM [auth j],
LF [auth H],
MM [auth j],
NC [auth B],
NF [auth I],
OF [auth I],
OL [auth d],
PF [auth I],
PL [auth d],
QF [auth I],
QL [auth d],
RF [auth I],
RJ [auth b],
SG [auth T],
SJ [auth b],
SN [auth x],
TE [auth D],
TG [auth U],
TJ [auth b],
TK [auth c],
TN [auth z],
UE [auth D],
UJ [auth b],
UK [auth c],
VA [auth A],
VF [auth J],
VJ [auth b],
VK [auth c],
WF [auth J],
WH [auth a],
WL [auth e],
XF [auth J],
YA [auth A],
YD [auth C],
YF [auth J],
YH [auth a]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 1.85 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.465α = 90
b = 228.176β = 90
c = 286.422γ = 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
Grants-in-Aid for Scientific ResearchJapanH24227002

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
  • Version 3.0: 2023-11-08
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
  • Version 3.1: 2024-10-23
    Changes: Structure summary
  • Version 4.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary