3HUO

X-ray crystallographic structure of CTX-M-9 S70G in complex with benzylpenicillin

• PDB DOI: https://doi.org/10.2210/pdb3HUO/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-15 Released: 2010-05-26 
• Deposition Author(s): Delmas, J., Leyssene, D., Dubois, D., Robin, F., Bonnet, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Dynamic view of the early and late steps of the catalytic mechanism mediated by the emerging enzymes CTX-M.

Delmas, J., Leyssene, D., Dubois, D., Birck, C., Samama, J.-P., Robin, F., Bonnet, R.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.91 kDa 
• Atom Count: 4,907 
• Modelled Residue Count: 522 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTX-M-9 extended-spectrum beta-lactamase	A, B	263	Escherichia coli	Mutation(s): 1  Gene Names: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9b EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli) Explore Q9L5C8  Go to UniProtKB:  Q9L5C8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNK	H [auth B]	(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C16 H20 N2 O5 S HCYWNSXLUZRKJX-RWMBFGLXSA-N
PNN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	PENICILLIN G C16 H18 N2 O4 S JGSARLDLIJGVTE-MBNYWOFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.205	α = 90
b = 106.784	β = 101.69
c = 47.645	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Delmas, J., Leyssene, D., Dubois, D., Robin, F., Bonnet, R.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-23
  Changes: Non-polymer description
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-11-01
  Changes: Data collection, Refinement description