2P74

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.88 Å
R-Value Free:
0.114 (Depositor), 0.120 (DCC)
R-Value Work:
0.100 (Depositor), 0.110 (DCC)
R-Value Observed:
0.100 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ja0712064
Primary Citation of Related Structures:
2P74

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L5C8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on 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), 0.120 (DCC)
R-Value Work: 0.100 (Depositor), 0.110 (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

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Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Chen, Y.

Bonnet, R.

Shoichet, B.K.

Revision History (Full details and data files)

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

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Help and Resources

2P74

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)