3G5J | pdb_00003g5j

Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb3G5J/pdb

• Classification: NUCLEOTIDE BINDING PROTEIN
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-05 Released: 2009-03-10 
• Deposition Author(s): Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.198 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630

Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.36 kDa 
• Atom Count: 2,393 
• Modeled Residue Count: 259 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ATP/GTP binding protein	A, B	134	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD1325
UniProt
Find proteins for Q18BI8 (Clostridioides difficile (strain 630)) Explore Q18BI8  Go to UniProtKB:  Q18BI8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A], E [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.76 Å
• R-Value Free:  0.198 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.489	α = 90
b = 60.192	β = 108.62
c = 79.107	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
SHELXCD	phasing
SHELXE	model building
CCP4	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing
ARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary