› 5v2c

X-ray diffraction
1.9Å resolution

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX

Released:
DOI: 10.2210/pdb5v2c/pdb
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PDB entry 5v2c coloured by chain, front view.
PDB entry 5v2c coloured by chain, side view.
PDB entry 5v2c coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.
Wiwczar JM, LaFountain AM, Wang J, Frank HA, Brudvig GW
Photosynth Res 134 175-182 (2017)
PMID: 28741056

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: 506 amino acids
Theoretical weight: 56.14 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-504; 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 HEC 2 x HEC

Cofactor: Ligand HEM 2 x HEM
24 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 6 x CL
Ligand BCT 3 x BCT
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand BCR 22 x BCR
Ligand PL9 4 x PL9
Ligand SQD 11 x SQD
Ligand LMG 14 x LMG
Ligand GOL 60 x GOL
Ligand LMT 18 x LMT
Ligand LHG 12 x LHG
Ligand PG4 57 x PG4
Ligand PGE 65 x PGE
Ligand P6G 17 x P6G
Ligand EDO 22 x EDO
Ligand CA 6 x CA
Ligand HTG 24 x HTG
Ligand 1PE 7 x 1PE
Ligand DGD 10 x DGD
Ligand MG 4 x MG
Ligand 2PE 1 x 2PE
Ligand PE8 1 x PE8
2 modified residues:
Ligand MHS 2 x MHS
Ligand FME 6 x FME

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 122.19Å b: 228.51Å c: 286.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.095 0.092 0.163

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Citations

1 review citation

The terminal enzymes of (bacterio)chlorophyll biosynthesis.
Proctor et al. (2022)
1 other article

4 mentions without citation

Structural basis of light-harvesting in the photosystem II core complex.
Müh et al. (2020)
3 more

PDB-REDO

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