7RL8

Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb7RL8/pdb

• Classification: HYDROLASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-07-23 Released: 2021-08-11 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Rosas-Lemus, M., Jedrzejczak, R., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630

Minasov, G., Shuvalova, L., Dubrovska, I., Rosas-Lemus, M., Jedrzejczak, R., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 117.41 kDa 
• Atom Count: 8,979 
• Modelled Residue Count: 1,005 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	255	Clostridioides difficile 630	Mutation(s): 1  Gene Names: CD630_04580 EC: 3.5.2.6
UniProt
Find proteins for Q188Q3 (Clostridioides difficile (strain 630)) Explore Q188Q3  Go to UniProtKB:  Q188Q3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth C], G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m37rl8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.118	α = 90
b = 93.878	β = 90
c = 138.346	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Rosas-Lemus, M., Jedrzejczak, R., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection