3G68

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.80 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3G68/pdb

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


• Deposited: 2009-02-06 Released: 2009-02-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Crystal structure of double-SIS domain protein (YP_001089791.1) from Clostridium difficile 630 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 81.49 kDa 
• Atom Count: 6,218 
• Modelled Residue Count: 696 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphosugar isomerase	A, B	352	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD3275, YP_001089791.1
UniProt
Find proteins for Q180C0 (Clostridioides difficile (strain 630)) Explore Q180C0  Go to UniProtKB:  Q180C0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], G [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33G68

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.525	α = 90
b = 55.914	β = 114.22
c = 103.031	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary