4RGK

Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 4RGK

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 47986.43

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized protein A 418 Yersinia pestis Gene Name(s): y1506 YP_2601 YPO2976
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.191
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 115.75 α = 90.00
b = 54.66 β = 124.47
c = 93.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-09-30
  • Released Date: 2014-12-31
  • Deposition author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2014-12-31

    Type: Initial release