3G5J

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.198
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q18BI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.172
R-Value Observed: 0.174
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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Help and Resources

3G5J

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)