3G13 | pdb_00003g13

Crystal structure of putative conjugative transposon recombinase from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb3G13/pdb

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


• Deposited: 2009-01-29 Released: 2009-02-10 
• Deposition Author(s): Bagaria, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of a putative conjugative transposon recombinase from Clostridium difficile

Bagaria, A., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 40.39 kDa 
• Atom Count: 2,554 
• Modeled Residue Count: 290 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative conjugative transposon recombinase	A, B	169	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD3370
UniProt
Find proteins for Q180L7 (Clostridioides difficile (strain 630)) Explore Q180L7  Go to UniProtKB:  Q180L7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.47	α = 90
b = 71.318	β = 90
c = 94.176	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Bagaria, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary