› 5b5e

X-ray diffraction
1.87Å resolution

Crystal structure analysis of Photosystem II complex

Released:
DOI: 10.2210/pdb5b5e/pdb
Model geometry
Fit model/data
PDB entry 5b5e coloured by chain, front view.
PDB entry 5b5e coloured by chain, side view.
PDB entry 5b5e coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II.
Tanaka A, Fukushima Y, Kamiya N
J Am Chem Soc 139 1718-1721 (2017)
PMID: 28102667

Function and Biology Details

Reaction catalysed: 
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112074 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 344 amino acids
Theoretical weight: 38.24 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P51765 (Residues: 1-344; Coverage: 96%)
Gene names: psbA, psbA-1
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 505 amino acids
Theoretical weight: 56.07 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-505; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Structure domains: Photosystem II CP47 reaction center protein
Photosystem II CP43 reaction center protein Chains: C, c
Photosystem II D2 protein Chains: D, d
Cytochrome b559 subunit alpha Chains: E, e
Cytochrome b559 subunit beta Chains: F, f
Photosystem II reaction center protein H Chains: H, h
Photosystem II reaction center protein I Chains: I, i
Photosystem II reaction center protein J Chains: J, j
Photosystem II reaction center protein K Chains: K, k
Photosystem II reaction center protein L Chains: L, l
Photosystem II reaction center protein M Chains: M, m
Photosystem II extrinsic protein O Chains: O, o
Photosystem II reaction center protein T Chains: T, t
Photosystem II extrinsic protein U Chains: U, u
Photosystem II extrinsic protein V Chains: V, v
Photosystem II reaction center protein Psb30 Chains: Y, y
Photosystem II reaction center protein X Chains: X, x
Photosystem II reaction center protein Z Chains: Z, z

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM

Cofactor: Ligand HEC 2 x HEC
19 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand BCR 20 x BCR
Ligand SQD 8 x SQD
Ligand PL9 4 x PL9
Ligand LHG 14 x LHG
Ligand UNL 53 x UNL
Ligand LMT 16 x LMT
Ligand DMS 112 x DMS
Ligand BCT 2 x BCT
Ligand CA 5 x CA
Ligand LMG 12 x LMG
Ligand HTG 20 x HTG
Ligand DGD 10 x DGD
Ligand RRX 2 x RRX
Ligand MG 2 x MG
1 modified residue:
Ligand FME 4 x FME

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 121.404Å b: 228.224Å c: 286.429Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.212

Quick links

Citations

7 review citations

Solar energy conversion by photosystem II: principles and structures.
Shevela et al. (2023)
6 more

5 mentions without citation

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function.
Hussein et al. (2023)
4 more