3LM8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 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 subtilisMutation(s): 1 
Gene Names: BSU15800thiNyloS
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
VIB
Query on VIB

Download CCD File 
A, B, C, D
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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

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: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 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
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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