3X30 | pdb_00003x30

Crystal structure of metallo-beta-lactamase from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3X30/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: 1.92 Å
• R-Value Free: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal structure of metallo-beta-lactamase 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: 25.22 kDa 
• Atom Count: 1,894 
• Modeled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0173 metal-dependent hydrolase TM_1162	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.727	α = 90
b = 98.727	β = 90
c = 45.255	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary