4MFG

2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.

• PDB DOI: https://doi.org/10.2210/pdb4MFG/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-27 Released: 2013-09-04 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Kudritska, M., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.

Minasov, G., Wawrzak, Z., Kudritska, M., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 73.69 kDa 
• Atom Count: 5,721 
• Modelled Residue Count: 672 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyltransferase	A, B, C, D	168	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_27480
UniProt
Find proteins for Q183I2 (Clostridioides difficile (strain 630)) Explore Q183I2  Go to UniProtKB:  Q183I2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	F [auth A], G [auth B], H [auth C], J [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG	E [auth A], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 6₃
• Diffraction Data: https://doi.org/10.18430/m34mfg

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.089	α = 90
b = 127.089	β = 90
c = 76.732	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Minasov, G., Wawrzak, Z., Kudritska, M., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description