5E2H | pdb_00005e2h

Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb5E2H/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2015-10-14 
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.7 kDa 
• Atom Count: 9,311 
• Modeled Residue Count: 1,062 
• Deposited Residue Count: 1,071 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C	357	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_3978 EC: 3.5.2.6
UniProt
Find proteins for A0QZC8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QZC8  Go to UniProtKB:  A0QZC8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.779	α = 90
b = 73.682	β = 90.19
c = 113.413	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-14 
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	United States	--

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