6YI4 | pdb_00006yi4

Structure of IMP-13 metallo-beta-lactamase complexed with citrate anion

PDB DOI: https://doi.org/10.2210/pdb6YI4/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-03-31 Released: 2020-04-08
Deposition Author(s): Zak, K.M., Zhou, R.X., Softley, C.A., Bostock, M.J., Sattler, M., Popowicz, G.M.
Funding Organization(s): European Union (EU), German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of IMP-13 metallo-beta-lactamase complexed with citrate anion

Zak, K.M., Zhou, R.X., Softley, C.A., Bostock, M.J., Sattler, M., Popowicz, G.M.

Not Published

Macromolecule Content

Total Structure Weight: 76.61 kDa
Atom Count: 5,644
Modeled Residue Count: 653
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth AAA], B [auth BBB], C [auth CCC]	226	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: bla-imp13, bla-IMP13, blaIMP-13 EC: 3.5.2.6
UniProt
Find proteins for Q7WYA8 (Pseudomonas aeruginosa) Explore Q7WYA8 Go to UniProtKB: Q7WYA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7WYA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain Q [auth CCC] SDF format, chain I [auth AAA] MOL2 format, chain Q [auth CCC] MOL2 format, chain I [auth AAA] mmCIF format, chain Q [auth CCC] mmCIF format, chain I [auth AAA]	I [auth AAA], Q [auth CCC]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain I [auth AAA] Focus chain Q [auth CCC] Interactions & Density Focus chain I [auth AAA] Focus chain Q [auth CCC]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain P [auth CCC] MOL2 format, chain P [auth CCC] mmCIF format, chain P [auth CCC]	P [auth CCC]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain P [auth CCC] Interactions & Density Focus chain P [auth CCC]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain R [auth CCC] SDF format, chain S [auth CCC] SDF format, chain O [auth BBB] SDF format, chain N [auth BBB] SDF format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain R [auth CCC] MOL2 format, chain S [auth CCC] MOL2 format, chain O [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain R [auth CCC] mmCIF format, chain S [auth CCC] mmCIF format, chain O [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain J [auth AAA]	J [auth AAA] K [auth AAA] N [auth BBB] O [auth BBB] R [auth CCC] J [auth AAA], K [auth AAA], N [auth BBB], O [auth BBB], R [auth CCC], S [auth CCC]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain R [auth CCC] Focus chain S [auth CCC] Interactions & Density Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain R [auth CCC] Focus chain S [auth CCC]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA]	D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB]	L [auth BBB], M [auth BBB]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth BBB] Focus chain M [auth BBB] Interactions & Density Focus chain L [auth BBB] Focus chain M [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.675	α = 90
b = 90.467	β = 100.853
c = 88.522	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union (EU)	Germany	675555
German Federal Ministry for Education and Research	Germany	GFPARV38

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description