6IAH | pdb_00006iah

Phosphatase Tt82 from Thermococcus thioreducens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.226 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 6IAH

This is version 1.1 of the entry. See complete history

Literature

A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity.

Havlickova, P.Brinsa, V.Brynda, J.Pachl, P.Prudnikova, T.Mesters, J.R.Kascakova, B.Kuty, M.Pusey, M.L.Ng, J.D.Rezacova, P.Smatanova, I.K.

(2019) Acta Crystallogr D Struct Biol 75: 743-752

  • DOI: https://doi.org/10.1107/S2059798319009586
  • Primary Citation Related Structures: 
    6IAH

  • PubMed Abstract: 

    The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg 2+ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P2 1 2 1 2, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.


  • Organizational Affiliation
    • Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 28.14 kDa 
  • Atom Count: 2,319 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hydrolase240Thermococcus thioreducensMutation(s): 0 
Gene Names: A3L14_07460AMR53_08235SAMN05216170_0457
UniProt
Find proteins for A0A0Q2QQ54 (Thermococcus thioreducens)
Explore A0A0Q2QQ54 
Go to UniProtKB:  A0A0Q2QQ54
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0Q2QQ54
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.226 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.33α = 90
b = 117β = 90
c = 33.83γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic17-24321S

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary