3HUO | pdb_00003huo

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.148 (Depositor), 0.147 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9L5C8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNK Query on PNK Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	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		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PNN Query on PNN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.148 (Depositor), 0.147 (DCC)
R-Value Observed: 0.150 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.