3OZH | pdb_00003ozh

Crystal Structure of Beta-Lactamase/D-alanine Carboxypeptidase from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3OZH/pdb

Classification: HYDROLASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-24 Released: 2010-10-20
Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.195 (Depositor), 0.186 (DCC)
R-Value Work:
0.160 (Depositor), 0.153 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3OZH

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

Literature

Crystal Structure of Beta-Lactamase/D-alanine Carboxypeptidase from Yersinia pestis

Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 38.65 kDa
Atom Count: 2,992
Modeled Residue Count: 351
Deposited Residue Count: 351
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase/D-alanine carboxypeptidase	A	351	Yersinia pestis CO92	Mutation(s): 0 Gene Names: ampH, y2964, YPO1224, YP_0915
UniProt
Find proteins for Q0WHI2 (Yersinia pestis) Explore Q0WHI2 Go to UniProtKB: Q0WHI2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0WHI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.195 (Depositor), 0.186 (DCC)
R-Value Work: 0.160 (Depositor), 0.153 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.069	α = 90
b = 75.8	β = 103.6
c = 59.08	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.