2ZWR

Crystal structure of TTHA1623 from thermus thermophilus HB8

• PDB DOI:  https://doi.org/10.2210/pdb2ZWR/pdb

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


• Deposited: 2008-12-17 Released: 2009-10-06 
• Deposition Author(s): Yamamura, A., Okada, A., Kameda, Y., Ohtsuka, J., Nakagawa, N., Ebihara, A., Yokoyama, S., Kuramitsu, S., Nagata, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8

Yamamura, A., Okada, A., Kameda, Y., Ohtsuka, J., Nakagawa, N., Ebihara, A., Nagata, K., Tanokura, M.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 455-459

• PubMed: 19407375 
• DOI: https://doi.org/10.1107/S174430910901361X
• Primary Citation of Related Structures:  
  2ZWR, 2ZZI


• PubMed Abstract: 
  

TTHA1623 is a metallo-beta-lactamase superfamily protein from the extremely thermophilic bacterium Thermus thermophilus HB8. Homologues of TTHA1623 exist in a wide range of bacteria and archaea and one eukaryote, Giardia lamblia, but their function remains unknown. To analyze the structural properties of TTHA1623, the crystal structures of its iron-bound and zinc-bound forms have been determined to 2.8 and 2.2 A resolution, respectively. TTHA1623 possesses an alphabetabetaalpha-fold similar to that of other metallo-beta-lactamase superfamily proteins with glyoxalase II-type metal coordination. However, TTHA1623 exhibits a putative substrate-binding pocket with a unique shape.

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Organizational Affiliation: 

Department of Applied Biological Chemistry, University of Tokyo, Yayoi, Bunkyo-ku, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.56 kDa 
• Atom Count: 3,233 
• Modelled Residue Count: 407 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase superfamily protein	A, B	207	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1623
UniProt
Find proteins for Q5SHV7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHV7  Go to UniProtKB:  Q5SHV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.136	α = 90
b = 114.122	β = 90
c = 114.711	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Yamamura, A., Okada, A., Kameda, Y., Ohtsuka, J., Nakagawa, N., Ebihara, A., Yokoyama, S., Kuramitsu, S., Nagata, K., Tanokura, M.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance