3X2Z

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (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

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Choi, H.J., Kim, H.J., Matsuura, A., Mikami, B., Yoon, H.J., Lee, H.H.

Revision History  

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