› 1dv3

X-ray diffraction
2.5Å resolution

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Released:
DOI: 10.2210/pdb1dv3/pdb
PDB entry 1dv3 coloured by chain, front view.
PDB entry 1dv3 coloured by chain, side view.
PDB entry 1dv3 coloured by chain, top view.
Source organism: Cereibacter sphaeroides
Primary publication:
Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.
Axelrod HL, Abresch EC, Paddock ML, Okamura MY, Feher G
Proc Natl Acad Sci U S A 97 1542-7 (2000)
PMID: 10677497

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142934 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Reaction center protein L chain Chains: L, R
Molecule details ›
Chains: L, R
Length: 281 amino acids
Theoretical weight: 31.35 KDa
Source organism: Cereibacter sphaeroides
UniProt:
  • Canonical: P0C0Y8 (Residues: 2-282; Coverage: 100%)
Gene name: pufL
Sequence domains: Photosynthetic reaction centre protein
Structure domains: Photosystem II protein D1-like
Reaction center protein M chain Chains: M, S
Molecule details ›
Chains: M, S
Length: 307 amino acids
Theoretical weight: 34.36 KDa
Source organism: Cereibacter sphaeroides
UniProt:
  • Canonical: P0C0Y9 (Residues: 2-308; Coverage: 100%)
Gene name: pufM
Sequence domains: Photosynthetic reaction centre protein
Structure domains: Photosystem II protein D1-like
Reaction center protein H chain Chains: H, T
Molecule details ›
Chains: H, T
Length: 260 amino acids
Theoretical weight: 28.14 KDa
Source organism: Cereibacter sphaeroides
UniProt:
  • Canonical: P0C0Y7 (Residues: 1-260; Coverage: 100%)
Gene name: puhA
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand BCL 8 x BCL
Ligand BPH 4 x BPH
Ligand U10 4 x U10
Ligand FE2 2 x FE2
Ligand CL 2 x CL
Ligand LDA 2 x LDA
Ligand CD 2 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P43212
Unit cell:
a: 141.25Å b: 141.25Å c: 275.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.226 0.252

Quick links

Citations

8 review citations

Voltage-gated proton channels and other proton transfer pathways.
Decoursey TE. (2003)
7 more

10 mentions without citation

Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.
Axelrod et al. (2000)
9 more