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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Kim, Y.Chhor, G.Endres, M.Babnigg, G.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
418Yersinia pestisMutation(s): 0 
Find proteins for A0A384LL35 (Yersinia pestis)
Go to UniProtKB:  A0A384LL35
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 115.750α = 90.00
b = 54.659β = 124.47
c = 93.152γ = 90.00
Software Package:
Software NamePurpose
SHELXEmodel building
HKL-3000phasing
SBC-Collectdata collection
HKL-3000data collection
SHELXCDphasing
HKL-3000data scaling
DMmodel building
HKL-3000data reduction
DMphasing
MLPHAREphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description