2ZO4 | pdb_00002zo4

Crystal structure of metallo-beta-lactamase family protein TTHA1429 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2ZO4/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-05 Released: 2009-03-17 
• Deposition Author(s): Yamamura, A., Nagata, K., Agari, Y., Ebihara, A., Nakagawa, N., Yokoyama, S., Kuramitsu, S., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8.

Yamamura, A., Ohtsuka, J., Kubota, K., Agari, Y., Ebihara, A., Nakagawa, N., Nagata, K., Tanokura, M.

(2008) Proteins 73: 1053-1057

• PubMed: 18767153 
• DOI: https://doi.org/10.1002/prot.22215
• Primary Citation Related Structures: 
  2ZO4

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 35.63 kDa 
• Atom Count: 2,621 
• Modeled Residue Count: 301 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase family protein	A	317	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1429 EC: 3
UniProt
Find proteins for Q5SIE5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIE5  Go to UniProtKB:  Q5SIE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.286	α = 90
b = 62.885	β = 90
c = 87.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Yamamura, A., Nagata, K., Agari, Y., Ebihara, A., Nakagawa, N., Yokoyama, S., Kuramitsu, S., Tanokura, M.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations