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X-ray diffraction
1.25Å resolution

STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE

Released:
DOI: 10.2210/pdb1otd/pdb
PDB entry 1otd coloured by chain, front view.
PDB entry 1otd coloured by chain, side view.
PDB entry 1otd coloured by chain, top view.
Source organism: Halorhodospira halophila
Primary publication:
Short hydrogen bonds in photoactive yellow protein.
Anderson S, Crosson S, Moffat K
Acta Crystallogr D Biol Crystallogr 60 1008-16 (2004)
PMID: 15159559

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147624 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Photoactive yellow protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 125 amino acids
Theoretical weight: 13.89 KDa
Source organism: Halorhodospira halophila
Expression system: Escherichia coli
UniProt:
  • Canonical: P16113 (Residues: 1-125; Coverage: 100%)
Gene name: pyp
Sequence domains: PAS fold
Structure domains: PAS domain

Ligands and Environments

1 bound ligand:
Ligand HC4 4 x HC4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P21
Unit cell:
a: 33.983Å b: 91.102Å c: 36.756Å
α: 90° β: 92.67° γ: 90°
R-values:
R R work R free
0.171 0.167 0.215
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Ligand-binding PAS domains in a genomic, cellular, and structural context.
Henry et al. (2011)
8 more

2 mentions without citation

Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.
Minasov et al. (2009)
1 more