5E2E | pdb_00005e2e

Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica

PDB DOI: https://doi.org/10.2210/pdb5E2E/pdb

Classification: HYDROLASE
Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-10-01 Released: 2015-10-28
Deposition Author(s): Kim, Y., Joachimiak, G., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.257 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5E2E

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica

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

To be published.

Macromolecule Content

Total Structure Weight: 58.29 kDa
Atom Count: 4,190
Modeled Residue Count: 520
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	269	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0 Gene Names: blaA, YE2019 EC: 3.5.2.6
UniProt
Find proteins for A1JML9 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JML9 Go to UniProtKB: A1JML9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1JML9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.257 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.116	α = 90
b = 93.513	β = 90
c = 122.219	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

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

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2022-04-13
Changes: Author supporting evidence, Data collection, Database references, Derived calculations
Version 1.2: 2024-10-16
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.