6XV5 | pdb_00006xv5

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem

PDB DOI: https://doi.org/10.2210/pdb6XV5/pdb

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

Deposited: 2020-01-21 Released: 2021-02-03
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.285 (Depositor), 0.283 (DCC)
R-Value Work:
0.213 (Depositor), 0.216 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 132.17 kDa
Atom Count: 8,700
Modeled Residue Count: 1,069
Deposited Residue Count: 1,166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase MrdA	A [auth BBB], B [auth AAA]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2W2Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
O2E Query on O2E	A [auth BBB], B [auth AAA]	L-PEPTIDE LINKING	C₂₅ H₃₂ N₄ O₉ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.285 (Depositor), 0.283 (DCC)
R-Value Work: 0.213 (Depositor), 0.216 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.265	α = 90
b = 147.772	β = 90
c = 164.523	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.