4ZEJ | pdb_00004zej

Crystal Structure of DIM-1 Metallo-beta-Lactamase exposed to Ceftazidime

PDB DOI: https://doi.org/10.2210/pdb4ZEJ/pdb

Classification: HYDROLASE
Organism(s): Stutzerimonas stutzeri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-20 Released: 2015-05-27
Deposition Author(s): Booth, M.P.S., Kosmopoulou, M., Spencer, J.
Funding Organization(s): British Society for Antimicrobial Chemotherapy

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.189 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Stricture of DIM-1 Metallo-beta-Lactamase

Booth, M.P.S., Kosmopoulou, M., Poirel, L., Nordmann, P., Spencer, J.

To be published.

Macromolecule Content

Total Structure Weight: 51.87 kDa
Atom Count: 3,640
Modeled Residue Count: 438
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase	A, B	232	Stutzerimonas stutzeri	Mutation(s): 0 Gene Names: blaDIM-1
UniProt
Find proteins for D5JGF6 (Stutzerimonas stutzeri) Explore D5JGF6 Go to UniProtKB: D5JGF6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5JGF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A], D [auth A], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.189 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.397	α = 90
b = 46.977	β = 90
c = 183.758	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Booth, M.P.S.

Kosmopoulou, M.

Spencer, J.

Funding Organization	Location	Grant Number
British Society for Antimicrobial Chemotherapy	United Kingdom	GA820

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description