3X2Z | pdb_00003x2z

Crystal structure of metallo-beta-lactamase in complex with nickel from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb3X2Z/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-07 Released: 2016-02-17
Deposition Author(s): Choi, H.J., Kim, H.J., Matsuura, A., Mikami, B., Yoon, H.J., Lee, H.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.205 (Depositor), 0.209 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3X2Z

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

Literature

Crystal structure of metallo-beta-lactamase in complex with nickel from Thermotoga maritima

Choi, H.J., Kim, H.J., Matsuura, A., Mikami, B., Yoon, H.J., Lee, H.H.

To be published.

Macromolecule Content

Total Structure Weight: 74.55 kDa
Atom Count: 5,534
Modeled Residue Count: 681
Deposited Residue Count: 681
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0173 metal-dependent hydrolase TM_1162	A, B, C	227	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_1162
UniProt
Find proteins for Q9X0P5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0P5 Go to UniProtKB: Q9X0P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth C] D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.205 (Depositor), 0.209 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.538	α = 90
b = 143.538	β = 90
c = 149.853	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.