4NMY

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

• PDB DOI: https://doi.org/10.2210/pdb4NMY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-15 Released: 2013-12-04 
• Deposition Author(s): Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.26 kDa 
• Atom Count: 5,221 
• Modelled Residue Count: 598 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type transport system, extracellular solute-binding protein	A, B	303	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_19790
UniProt
Find proteins for Q187U0 (Clostridioides difficile (strain 630)) Explore Q187U0  Go to UniProtKB:  Q187U0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIB	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
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m34nmy

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.529	α = 90
b = 76.867	β = 90
c = 154.901	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Kim, Y., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release