4JJP

2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.056 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630

Halavaty, A.S.Wawrzak, Z.Onopriyenko, O.Grimshaw, S.Savchenko, A.Anderson, W.F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphomethylpyrimidine kinase
A, B
267Peptoclostridium difficile (strain 630)Mutation(s): 0 
Gene Names: thiD
Find proteins for Q186F5 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q186F5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 56.751α = 90.00
b = 79.741β = 90.00
c = 92.863γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description