3MBH

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative phosphomethylpyrimidine kinase
A, B, C, D, E, F
291Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)EC: 2.7.1.35
Find proteins for Q89ZB9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q89ZB9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PXL
Query on PXL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
PYRIDOXAL
C8 H9 N O3
RADKZDMFGJYCBB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 93.723α = 90.00
b = 138.368β = 90.00
c = 143.539γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
SHELXDphasing
REFMACrefinement
XDSdata reduction
SHELXphasing
PDB_EXTRACTdata extraction
MolProbitymodel building
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description