6VBM

Crystal structure of a S310A mutant of PBP2 from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb6VBM/pdb

Classification: HYDROLASE
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-12-19 Released: 2020-04-15
Deposition Author(s): Singh, A., Davies, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.222
R-Value Work: 0.194
R-Value Observed: 0.195

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

Literature

Mutations in Neisseria gonorrhoeae penicillin-binding protein 2 associated with extended-spectrum cephalosporin resistance create an energetic barrier against acylation via restriction of protein dynamics

Singh, A., Turner, J., Tomberg, J., Fedarovich, A., Unemo, M., Nicholas, R.A., Davies, C.

(2020) J Biol Chem

Macromolecule Content

Total Structure Weight: 70.81 kDa
Atom Count: 5,065
Modelled Residue Count: 640
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peptidoglycan D,D-transpeptidase PenA	A, B	329	Neisseria gonorrhoeae	Mutation(s): 1 Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for P08149 (Neisseria gonorrhoeae) Explore P08149 Go to UniProtKB: P08149
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B]	C [auth B], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.222
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.594	α = 90
b = 77.007	β = 92.34
c = 87.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
FFT	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM066861

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.