6TII | pdb_00006tii

Crystal structure of penicillin-binding protein 2 from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb6TII/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-22 Released: 2020-12-02
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.253 (Depositor), 0.270 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structure of penicillin-binding protein 2 from Yersinia pestis

Pankov, G.

To be published.

Macromolecule Content

Total Structure Weight: 131.27 kDa
Atom Count: 8,753
Modeled Residue Count: 1,068
Deposited Residue Count: 1,166
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase MrdA	A [auth AAA], B [auth BBB]	583	Yersinia pestis	Mutation(s): 0 Gene Names: mrdA, YPO2604 EC: 3.4.16.4
UniProt
Find proteins for A0A0H2W2Y2 (Yersinia pestis) Explore A0A0H2W2Y2 Go to UniProtKB: A0A0H2W2Y2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2W2Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth BBB]	C [auth AAA], D [auth BBB]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.253 (Depositor), 0.270 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.661	α = 113.467
b = 84.773	β = 94.972
c = 88.359	γ = 103.725

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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.