6VBL | pdb_00006vbl

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02

PDB DOI: https://doi.org/10.2210/pdb6VBL/pdb

Classification: HYDROLASE
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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: 1.93 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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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 Biological Chem

Macromolecule Content

Total Structure Weight: 35.33 kDa
Atom Count: 2,560
Modeled Residue Count: 324
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peptidoglycan D,D-transpeptidase PenA	A	330	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for Q8RR30 (Neisseria gonorrhoeae) Explore Q8RR30 Go to UniProtKB: Q8RR30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RR30
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.183 (Depositor), 0.189 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.621	α = 90
b = 61.085	β = 90
c = 109.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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

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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.