7BN9 | pdb_00007bn9

Crystal Structure of Bacillus subtilis Penicillin Binding Protein 3

PDB DOI: https://doi.org/10.2210/pdb7BN9/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-01-21 Released: 2022-03-02
Deposition Author(s): Rao, V.A., Lewis, R.J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.269 (Depositor), 0.275 (DCC)
R-Value Work:
0.213 (Depositor), 0.219 (DCC)
R-Value Observed:
0.216 (Depositor)

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

Literature

Cooperation between peptidoglycan transpeptidases and SEDS proteins in Bacillus subtilis cell division

Sassine, J., Rao, V.A., Goldsmith, G., Breukink, E., Lewis, R.J., Daniel, R.A., Vollmer, W.

To be published.

Macromolecule Content

Total Structure Weight: 148.04 kDa
Atom Count: 9,279
Modeled Residue Count: 1,208
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A, B	662	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: pbpC, ycsM, yzsA, BSU04140 EC: 3.4.16.4
UniProt
Find proteins for P42971 (Bacillus subtilis (strain 168)) Explore P42971 Go to UniProtKB: P42971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42971
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.269 (Depositor), 0.275 (DCC)
R-Value Work: 0.213 (Depositor), 0.219 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.624	α = 90
b = 108.684	β = 90
c = 238.691	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N002679/1

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.