1S5L

Architecture of the photosynthetic oxygen evolving center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.296 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Architecture of the Photosynthetic Oxygen-Evolving Center

Ferreira, K.N.Iverson, T.M.Maghlaoui, K.Barber, J.Iwata, S.

(2004) Science 303: 1831-1838

  • DOI: 10.1126/science.1093087

  • PubMed Abstract: 
  • Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We hav ...

    Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.


    Organizational Affiliation

    Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem Q(B) protein
A, a
344Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbA1 (psbA-1)
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A444
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
photosystem II core light harvesting protein
B, b
510Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
photosystem II CP43 protein
C, c
473Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
photosystem II reaction center D2 protein
D, d
352Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbD1, psbD2
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 alpha subunit
E, e
84Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 beta subunit
F, f
45Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbH protein
H, h
66Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ43
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center I protein
I, i
38Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJZ6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center J protein
J, j
40Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P59087
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center L protein
L, l
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center M protein
M, m
36Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHA7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
246Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A431
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbT protein
T, t
32Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbT
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
134Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbU
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1L5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A386
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbX protein
X, x
50Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbX
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1R6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II PsbN protein
N, n
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center Z protein
Z, z
62Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbZ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHJ2
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download SDF File 
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

Download SDF File 
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
BCT
Query on BCT

Download SDF File 
Download CCD File 
A, a, d, D
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
a, A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
BCR
Query on BCR

Download SDF File 
Download CCD File 
B, b, C, c, d, F, J, j, K, k
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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

Download SDF File 
Download CCD File 
B, d
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEC
Query on OEC

Download SDF File 
Download CCD File 
A, a
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
n, N
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.296 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 134.992α = 90.00
b = 228.849β = 90.00
c = 309.940γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-25
    Type: Non-polymer description