4JXG

Crystal Structure of AmpC beta-lactamase from E. coli in Complex with Oxacillin

PDB DOI: https://doi.org/10.2210/pdb4JXG/pdb

Classification: hydrolase/antibiotic
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-28 Released: 2014-10-29
Deposition Author(s): Wallar, B.J., Powers, R.A., Docter, B.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.185
R-Value Work: 0.151
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Complexed structures of AmpC beta-lactamase

Docter, B.E., Baggett, V.L., Powers, R.A., Wallar, B.J.

To be published.

Macromolecule Content

Total Structure Weight: 80.42 kDa
Atom Count: 6,272
Modelled Residue Count: 716
Deposited Residue Count: 716
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	A [auth B], B [auth A]	358	Escherichia coli K-12	Mutation(s): 0 Gene Names: ampC, ampA, b4150, JW4111 EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811 Go to UniProtKB: P00811
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00811
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1S6 Query on 1S6 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth A]	D [auth B], E [auth A]	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid C₁₉ H₂₁ N₃ O₅ S QXXMSXCGXIRLPM-ISTRZQFTSA-N		Interactions Focus chain D [auth B] Focus chain E [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.185
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.856	α = 90
b = 76.868	β = 117.01
c = 97.845	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-29

Deposition Author(s):

Wallar, B.J.

Powers, R.A.

Docter, B.E.

Revision History (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary

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Help and Resources

4JXG

Crystal Structure of AmpC beta-lactamase from E. coli in Complex with Oxacillin

Complexed structures of AmpC beta-lactamase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2