› 1v9f

X-ray diffraction
1.7Å resolution

Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli

Released:
DOI: 10.2210/pdb1v9f/pdb
PDB entry 1v9f coloured by chain, front view.
PDB entry 1v9f coloured by chain, side view.
PDB entry 1v9f coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.
Mizutani K, Machida Y, Unzai S, Park SY, Tame JR
Biochemistry 43 4454-63 (2004)
PMID: 15078091

Function and Biology Details

Reaction catalysed: 
23S rRNA uridine(1911)/uridine(1915)/uridine(1917) = 23S rRNA pseudouridine(1911)/pseudouridine(1915)/pseudouridine(1917)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152625 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal large subunit pseudouridine synthase D Chain: A
Molecule details ›
Chain: A
Length: 325 amino acids
Theoretical weight: 37.05 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P33643 (Residues: 2-326; Coverage: 100%)
Gene names: JW2576, b2594, rluD, sfhB, yfiI
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P6522
Unit cell:
a: 74.506Å b: 74.506Å c: 265.009Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.2 0.224
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Pseudouridine synthases.
Hamma et al. (2006)
5 more

2 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
1 more