9ENV | pdb_00009env

Apo GES-1 beta-Lactamase Crystallised with Citric Acid

PDB DOI: https://doi.org/10.2210/pdb9ENV/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-13 Released: 2025-03-26
Deposition Author(s): Beer, M., Hinchliffe, P., Spencer, J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Apo GES-1 beta-Lactamase Crystallised with Citric Acid

Beer, M., Hinchliffe, P., Spencer, J.

To be published.

Macromolecule Content

Total Structure Weight: 63.42 kDa
Atom Count: 4,752
Modeled Residue Count: 537
Deposited Residue Count: 578
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, B	289	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: ges-1, blaGES-1 EC: 3.5.2.6
UniProt
Find proteins for Q09HD0 (Klebsiella pneumoniae) Explore Q09HD0 Go to UniProtKB: Q09HD0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09HD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209 (Depositor), 0.209 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.564	α = 90
b = 80.814	β = 90
c = 104.543	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T008741/10

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

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.