6CTY

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution.

Lipowska, J.Shabalin, I.G.Anderson, W.F.Minor, W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotase
A, B, C, D, E, F
372Yersinia pestisMutation(s): 0 
Gene Names: pyrC
EC: 3.5.2.3
Find proteins for Q8ZFU4 (Yersinia pestis)
Go to UniProtKB:  Q8ZFU4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MLT
Query on MLT

Download SDF File 
Download CCD File 
A, B, C, D, F
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
CSX
Query on CSX
A, B, C, D, E, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.838α = 90.00
b = 112.202β = 90.00
c = 208.264γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-3000data scaling
HKL-3000data reduction
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
LAUEGENdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States--

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references