8U00

Crystal structure of metallo-beta-lactamase superfamily protein from Caulobacter vibrioides

PDB DOI: https://doi.org/10.2210/pdb8U00/pdb

Classification: HYDROLASE
Organism(s): Caulobacter vibrioides CB15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-28 Released: 2023-09-27
Deposition Author(s): Kim, Y., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of metallo-beta-lactamase superfamily protein from Caulobacter vibrioides

Kim, Y., Maltseva, N., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 59.21 kDa
Atom Count: 3,928
Modelled Residue Count: 484
Deposited Residue Count: 542
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 superfamily protein	A, B	271	Caulobacter vibrioides CB15	Mutation(s): 0 Gene Names: CC_2139
UniProt
Find proteins for Q9A6F5 (Caulobacter vibrioides (strain ATCC 19089 / CB15)) Explore Q9A6F5 Go to UniProtKB: Q9A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9A6F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	D [auth A] E [auth A] F [auth A] M [auth B] N [auth B] D [auth A], E [auth A], F [auth A], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B]	C [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	K [auth A], S [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	H [auth A], I [auth A], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B]	G [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]