2P74 | pdb_00002p74

CTX-M-9 class A beta-lactamase apo crystal structure at 0.88 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2P74/pdb

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


• Deposited: 2007-03-19 Released: 2007-04-24 
• Deposition Author(s): Chen, Y., Bonnet, R., Shoichet, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.88 Å
• R-Value Free: 
  0.114 (Depositor), 0.117 (DCC) 
• R-Value Work: 
  0.100 (Depositor), 0.105 (DCC) 
• R-Value Observed: 
  0.100 (Depositor) 

Starting Model: experimental

Literature

The Acylation Mechanism of CTX-M beta-Lactamase at 0.88 A Resolution.

Chen, Y., Bonnet, R., Shoichet, B.K.

(2007) J Am Chem Soc 129: 5378-5380

• PubMed: 17408273 
• DOI: https://doi.org/10.1021/ja0712064
• Primary Citation Related Structures: 
  2P74

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.46 kDa 
• Atom Count: 5,395 
• Modeled Residue Count: 523 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase CTX-M-9a	A, B	263	Escherichia coli	Mutation(s): 0  Gene Names: CTX-M 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
PO4	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.88 Å
• R-Value Free:  0.114 (Depositor), 0.117 (DCC) 
• R-Value Work:  0.100 (Depositor), 0.105 (DCC) 
• R-Value Observed: 0.100 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.162	α = 90
b = 106.796	β = 102.09
c = 47.785	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Chen, Y., Bonnet, R., Shoichet, B.K.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-30
  Changes: Structure summary