4NMY

Crystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Crystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile

Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-type transport system, extracellular solute-binding protein
A, B
303Clostridioides difficile 630Mutation(s): 0 
Gene Names: CD630_19790
UniProt
Find proteins for Q187U0 (Clostridioides difficile (strain 630))
Explore Q187U0 
Go to UniProtKB:  Q187U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ187U0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIB
Query on VIB
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.529α = 90
b = 76.867β = 90
c = 154.901γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VIBClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary