3LM8

Crystal Structure of Thiamine pyrophosphokinase from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR677


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Northeast Structural Genomics Consortium Target SR677

Kuzin, A.Abashidze, M.Seetharaman, J.Mao, M.Xiao, R.Foote, E.L.Ciccosanti, C.Wang, H.Everett, J.K.Nair, R.Acton, T.B.Rost, B.Montelione, G.T.Hunt, J.F.Tong, L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiamine pyrophosphokinase
A, B, C, D
222Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: thiN (yloS)
EC: 2.7.6.2
Find proteins for O34664 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34664
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
VIB
Query on VIB

Download SDF File 
Download CCD File 
A, B, C, D
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
THIAMIN, VITAMIN B1
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.943α = 82.89
b = 62.153β = 82.02
c = 84.161γ = 87.61
Software Package:
Software NamePurpose
HKL-2000data reduction
BALBESphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description