Macromolecule Content

Total Structure Weight: 116.70 kDa
Atom Count: 9311
Modelled Residue Count: 1062
Deposited Residue Count: 1071
Unique protein chains: 1

5E2H

Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis

PDB DOI: 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QZC8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C]	J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C]	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.164
R-Value Observed: 0.165
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

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

Deposition Author(s):

Hatzos-Skintges, C.

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.