1Z9D

Crystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes

Rajashankar, K.R.Kniewel, R.Lee, K.Lima, C.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
uridylate kinaseA, B, C252Streptococcus pyogenesMutation(s): 9 
Gene Names: pyrH
EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
Find proteins for P65938 (Streptococcus pyogenes serotype M1)
Explore P65938 
Go to UniProtKB:  P65938
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth B] , I [auth B] , J [auth B] , K [auth C] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth B],  I [auth B],  J [auth B],  K [auth C],  L [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.288α = 90
b = 57.309β = 90
c = 94.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary