6VBD

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by ceftriaxone

• PDB DOI: https://doi.org/10.2210/pdb6VBD/pdb

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


• Deposited: 2019-12-18 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.85 kDa 
• Atom Count: 2,649 
• Modelled Residue Count: 324 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

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 F2Z7K9 (Neisseria gonorrhoeae) Explore F2Z7K9  Go to UniProtKB:  F2Z7K9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEF	B [auth A]	CEFOTAXIME, C3' cleaved, open, bound form C14 H15 N5 O5 S2 NRYMPLKBKFIWQC-YVCCLBOHSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.311	α = 90
b = 60.682	β = 90
c = 109.344	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Singh, A., Davies, C.

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

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release