4IL6

Structure of Sr-substituted photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 110: 3889-3894

  • DOI: 10.1073/pnas.1219922110

  • 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 elu ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem Q(B) protein
A, a
334Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbA (psbA-1)
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II core light harvesting protein
B, b
505Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 protein
C, c
451Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
80Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12238 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12238
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12239 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12239
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
63Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P19052 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19052
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q7DGD4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P19054 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19054
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12241 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12241
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
34Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12312 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12312
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
244Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
31Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P12313 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12313
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
97Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P56152 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P56152
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12 (psbY)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein Y
R
34Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DKM3 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKM3
Small Molecules
Ligands 18 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

Download SDF File 
Download CCD File 
A, a, B, b, c, D, f
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
OER
Query on OER

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Download CCD File 
a, A
SR-MN4-O5 CLUSTER
Mn4SrOt5-cluster
Mn4 O5 Sr
CSESTIVEXPKVIG-UHFFFAOYSA-N
 Ligand Interaction
CLA
Query on CLA

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Download CCD File 
a, A, B, b, c, C, D, d
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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Download CCD File 
A, a, d, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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a, A, B, b, D, d, v, V
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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B, b, c, C, D, d, o, V
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
DGD
Query on DGD

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Download CCD File 
c, C, H, h
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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Download CCD File 
a, A, B, C, c, D, d, m, Z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

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Download CCD File 
D, d
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
J, j, k, K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
F, f, V, v
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
A, a, b, B, C, c, D, d, h, H, J, k, K, T, t, y
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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Download CCD File 
A, a, D
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
a, A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
A, a, B, b, C, f, i, m, M, t
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
a, A, B, b, C, c, D, d, O, U, u, V, v
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
b, B, D, d, E, e
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
I, i, m, M, T, t, Z, z
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 121.860α = 90.00
b = 228.790β = 90.00
c = 285.760γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSphasing
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description