6UE2

1.85 Angstrom Resolution Crystal Structure of Class D beta-lactamase from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb6UE2/pdb

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


• Deposited: 2019-09-20 Released: 2019-12-25 
• 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: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

1.85 Angstrom Resolution Crystal Structure 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: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 118.6 kDa 
• Atom Count: 9,280 
• Modelled Residue Count: 1,007 
• 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): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PPI	G [auth C]	PROPANOIC ACID C3 H6 O2 XBDQKXXYIPTUBI-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.983	α = 90
b = 93.2	β = 90
c = 137.583	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
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: 2019-12-25
  Type: Initial release