5E2G | pdb_00005e2g

Crystal Structure of D-alanine Carboxypeptidase AmpC from Burkholderia cenocepacia

• PDB DOI: https://doi.org/10.2210/pdb5E2G/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2015-10-14 
• Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal Structure of D-alanine Carboxypeptidase AmpC from Burkholderia cenocepacia

Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 79.79 kDa 
• Atom Count: 6,057 
• Modeled Residue Count: 694 
• Deposited Residue Count: 722 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	361	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: ampC, BCAS0156 EC: 3.5.2.6
UniProt
Find proteins for B4EPS2 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EPS2  Go to UniProtKB:  B4EPS2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	F [auth A], J [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
SCN	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

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: 1.65 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.965	α = 90
b = 85.965	β = 90
c = 90.399	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary