5EVL

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb5EVL/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-11-19 Released: 2015-12-02 
• Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.181 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Literature

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum

Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.97 kDa 
• Atom Count: 3,093 
• Modelled Residue Count: 355 
• Deposited Residue Count: 373 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	373	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: ampC, CV_1310 EC: 3.5.2.6
UniProt
Find proteins for Q7NYG4 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NYG4  Go to UniProtKB:  Q7NYG4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.181 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.604	α = 90
b = 59.262	β = 98.18
c = 59.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Data collection, Derived calculations