5BXG | pdb_00005bxg

Crystal structure of an uncharacterized beta-sandwich protein (CD630_09570) from Clostridium difficile 630 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5BXG/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-08 Released: 2015-07-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of an uncharacterized beta-sandwich protein (CD630_09570) from Clostridium difficile 630 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content 

• Total Structure Weight: 18.76 kDa 
• Atom Count: 1,511 
• Modeled Residue Count: 151 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized beta-sandwich protein	A	162	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_09570, CD630_29070, CDIF630_03179, YP_001087438.1
UniProt
Find proteins for Q183Z1 (Clostridioides difficile (strain 630)) Explore Q183Z1  Go to UniProtKB:  Q183Z1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35BXG

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.108	α = 90
b = 69.108	β = 90
c = 87.802	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data scaling
XSCALE	data scaling
SHELX	phasing
SHARP	phasing
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary