4IL6

Structure of Sr-substituted photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.3 of the entry. See complete history


Literature

Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation

Koua, F.H.Umena, Y.Kawakami, K.Shen, J.R.

(2013) Proc Natl Acad Sci U S A 110: 3889-3894

  • DOI: 10.1073/pnas.1219922110
  • Primary Citation of Related Structures:  
    4IL6

  • PubMed Abstract: 
  • Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2 ...

    Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 Å, and compared it with the 1.9 Å structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca(2+), resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca(2+), W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr(2+)-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 Å structure of native PSII, was found in the Sr-PSII structure.


    Organizational Affiliation

    Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
U [auth a]
334Thermostichus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth b]
505Thermostichus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth c]
451Thermostichus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [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,
Y [auth e]
80Thermostichus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
34Thermostichus 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],
AA [auth h]
63Thermostichus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
BA [auth i]
36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J],
CA [auth j]
37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K],
DA [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 LK [auth L],
EA [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 ML [auth M],
FA [auth m]
34Thermostichus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O],
GA [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 TN [auth T],
HA [auth t]
31Thermostichus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U],
IA [auth u]
97Thermostichus 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-550P [auth V],
JA [auth v]
137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ycf12Q [auth Y],
KA [auth y]
30Thermostichus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
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 XR [auth X],
LA [auth x]
40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z],
MA [auth z]
62Thermostichus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbYtsl0836
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 19 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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CD [auth C],
DD [auth C],
DI [auth c],
ED [auth C],
EI [auth c],
CD [auth C],
DD [auth C],
DI [auth c],
ED [auth C],
EI [auth c],
FI [auth c],
LE [auth H],
OJ [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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AD [auth C],
AI [auth c],
BI [auth c],
GB [auth B],
HB [auth B],
AD [auth C],
AI [auth c],
BI [auth c],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth B],
JG [auth b],
KB [auth B],
KG [auth b],
LB [auth B],
LG [auth b],
MB [auth B],
MG [auth b],
NB [auth B],
NG [auth b],
OB [auth B],
OC [auth C],
OG [auth b],
PB [auth B],
PC [auth C],
PG [auth b],
PH [auth c],
QB [auth B],
QC [auth C],
QD [auth D],
QG [auth b],
QH [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RD [auth D],
RG [auth b],
RH [auth c],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth a],
SG [auth b],
SH [auth c],
TB [auth B],
TC [auth C],
TD [auth D],
TF [auth a],
TG [auth b],
TH [auth c],
TI [auth d],
UA [auth A],
UB [auth B],
UC [auth C],
UF [auth a],
UG [auth b],
UH [auth c],
UI [auth d],
VB [auth B],
VC [auth C],
VG [auth b],
VH [auth c],
WC [auth C],
WG [auth b],
WH [auth c],
XC [auth C],
XF [auth a],
XG [auth b],
XH [auth c],
YC [auth C],
YG [auth b],
YH [auth c],
ZC [auth C],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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SD [auth D],
TA [auth A],
VF [auth a],
WF [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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CB [auth A],
CH [auth b],
GI [auth c],
LJ [auth f],
MF [auth a],
CB [auth A],
CH [auth b],
GI [auth c],
LJ [auth f],
MF [auth a],
WD [auth D],
XA [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
 Ligand Interaction
LMG
Query on LMG

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AE [auth D],
AG [auth a],
AJ [auth d],
BC [auth B],
FD [auth C],
AE [auth D],
AG [auth a],
AJ [auth d],
BC [auth B],
FD [auth C],
GD [auth C],
HI [auth c],
II [auth c],
JI [auth c],
LF [auth Z],
YA [auth A],
YJ [auth m]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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VD [auth D],
WA [auth A],
WI [auth d],
ZF [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
 Ligand Interaction
LHG
Query on LHG

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AC [auth B],
DH [auth b],
IE [auth E],
JJ [auth e],
XD [auth D],
AC [auth B],
DH [auth b],
IE [auth E],
JJ [auth e],
XD [auth D],
XI [auth d],
YD [auth D],
YI [auth d],
ZD [auth D],
ZI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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CF [auth V],
FK [auth v],
JE [auth F],
KJ [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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AF [auth T],
AH [auth b],
BD [auth C],
BH [auth b],
BK [auth t],
AF [auth T],
AH [auth b],
BD [auth C],
BH [auth b],
BK [auth t],
CI [auth c],
JK [auth y],
KE [auth H],
NJ [auth h],
OE [auth J],
RE [auth K],
SE [auth K],
TJ [auth k],
UD [auth D],
UJ [auth k],
VA [auth A],
VI [auth d],
WB [auth B],
XB [auth B],
YB [auth B],
YF [auth a],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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BG [auth a],
CC [auth B],
DB [auth A],
DK [auth t],
EB [auth A],
BG [auth a],
CC [auth B],
DB [auth A],
DK [auth t],
EB [auth A],
EH [auth b],
HD [auth C],
KH [auth b],
MJ [auth f],
NF [auth a],
QJ [auth i],
WE [auth M],
XE [auth M],
XJ [auth m],
ZJ [auth m]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OER
Query on OER

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NA [auth A],
OF [auth a]
SR-MN4-O5 CLUSTER
Mn4 O5 Sr
CSESTIVEXPKVIG-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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AK [auth o],
BE [auth D],
BJ [auth d],
DC [auth B],
DF [auth V],
AK [auth o],
BE [auth D],
BJ [auth d],
DC [auth B],
DF [auth V],
FH [auth b],
GG [auth b],
HC [auth B],
HE [auth D],
HG [auth b],
HJ [auth d],
IC [auth B],
ID [auth C],
JD [auth C],
JH [auth b],
KI [auth c],
NI [auth c]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
GOL
Query on GOL

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FB [auth A],
FF [auth V],
FG [auth a],
GE [auth D],
GJ [auth d],
FB [auth A],
FF [auth V],
FG [auth a],
GE [auth D],
GJ [auth d],
HF [auth V],
HK [auth v],
IF [auth V],
IJ [auth d],
IK [auth v],
KC [auth B],
LH [auth b]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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AB [auth A],
BF [auth U],
CG [auth a],
DG [auth a],
EE [auth D],
AB [auth A],
BF [auth U],
CG [auth a],
DG [auth a],
EE [auth D],
EF [auth V],
EJ [auth d],
EK [auth u],
FC [auth B],
FE [auth D],
FJ [auth d],
GC [auth B],
GF [auth V],
GK [auth v],
HH [auth b],
IH [auth b],
KD [auth C],
LC [auth B],
LD [auth C],
MC [auth B],
MD [auth C],
MH [auth b],
MI [auth c],
NC [auth B],
ND [auth C],
NH [auth b],
OD [auth C],
OH [auth b],
OI [auth c],
PI [auth c],
QI [auth c],
RI [auth c],
YE [auth O],
ZA [auth A],
ZE [auth O]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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PD [auth D],
SI [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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OA [auth A],
PF [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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PA [auth A],
QA [auth A],
QF [auth a],
RF [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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QE [auth J],
SJ [auth j],
UE [auth K],
VJ [auth k]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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BB [auth A],
CE [auth D],
CJ [auth d],
CK [auth t],
DE [auth D],
BB [auth A],
CE [auth D],
CJ [auth d],
CK [auth t],
DE [auth D],
DJ [auth d],
EC [auth B],
EG [auth a],
GH [auth b],
IG [auth b],
JC [auth B],
JF [auth Y],
KF [auth X],
KK [auth y],
LI [auth c],
LK [auth x],
ME [auth I],
NE [auth I],
PE [auth J],
PJ [auth i],
RJ [auth j],
TE [auth K],
VE [auth L],
WJ [auth l]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
BA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.86α = 90
b = 228.79β = 90
c = 285.76γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary