6TUD | pdb_00006tud

Crystal structure of Y. pestis penicillin-binding protein 3

PDB DOI: https://doi.org/10.2210/pdb6TUD/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-06 Released: 2021-01-27
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.276 (Depositor), 0.279 (DCC)
R-Value Work:
0.244 (Depositor), 0.248 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

The structure of penicillin-binding protein 3 from Yersinia pestis

Pankov, G.

To be published.

Macromolecule Content

Total Structure Weight: 119.12 kDa
Atom Count: 7,046
Modeled Residue Count: 928
Deposited Residue Count: 1,098
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A [auth AAA], B [auth BBB]	549	Yersinia pestis	Mutation(s): 0 Gene Names: ftsI, YPO0549 EC: 3.4.16.4
UniProt
Find proteins for A0A3N4B5A3 (Yersinia pestis) Explore A0A3N4B5A3 Go to UniProtKB: A0A3N4B5A3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N4B5A3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.276 (Depositor), 0.279 (DCC)
R-Value Work: 0.244 (Depositor), 0.248 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.8	α = 90
b = 100.8	β = 90
c = 314.409	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-01-27
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.