6HR9 | pdb_00006hr9

Nitrocefin acylation of both catalytic serines of the Y409 mutant of penicillin-binding protein 3 from P. aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6HR9/pdb

• Classification: PENICILLIN-BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-26 Released: 2019-10-23 
• Deposition Author(s): Bellini, D., Dowson, C.G.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Nitrocefin acylation of both catalytic serines of penicillin-binding protein 3 from P. aeruginosa

Bellini, D., Dowson, C.G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.85 kDa 
• Atom Count: 3,900 
• Modeled Residue Count: 491 
• Deposited Residue Count: 535 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A	535	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: ftsI, pbpB, PA4418 EC: 3.4.16.4
UniProt
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XD46  Go to UniProtKB:  G3XD46

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NEF (Subject of Investigation/LOI)	B [auth A], C [auth A]	Nitrocefin - open form C21 H18 N4 O9 S2 PYBZXZZHQKFSGC-CZHQAMEJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.042	α = 90
b = 83.261	β = 90
c = 88.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Bellini, D., Dowson, C.G.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	grant.MR/P007503/1

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 2.0: 2021-08-25
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 3.0: 2022-07-20
  Type: Coordinate replacement
  Reason: Chirality error
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 3.1: 2024-01-24
  Changes: Data collection, Refinement description
• Version 3.2: 2024-11-20
  Changes: Structure summary