4HPE

Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb4HPE/pdb

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


• Deposited: 2012-10-23 Released: 2012-11-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 203.84 kDa 
• Atom Count: 13,970 
• Modelled Residue Count: 1,735 
• Deposited Residue Count: 1,848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cell wall hydrolase Tn916-like,CTn1-Orf17	A, B, C, D, E, F	308	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_03720, YP_001086839.1
UniProt
Find proteins for Q18DB2 (Clostridioides difficile (strain 630)) Explore Q18DB2  Go to UniProtKB:  Q18DB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth A], L [auth A], N [auth B], Q [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], O [auth C], P [auth D], R [auth E], S [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A, B, C, D, E, F	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M34HPE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.522	α = 109.71
b = 101.211	β = 108.86
c = 101.436	γ = 101.36

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-20
  Changes: Data collection, Refinement description