2GM7 | pdb_00002gm7

TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum

• PDB DOI: https://doi.org/10.2210/pdb2GM7/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrobaculum aerophilum str. IM2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-04-06 Released: 2006-04-18 
• Deposition Author(s): Sawaya, M.R., Chan, S., Han, G.W., Perry, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Ten A Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum

Sawaya, M.R., Chan, S., Han, G.W., Perry, L.J., Yeates, T.O.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 102.19 kDa 
• Atom Count: 6,931 
• Modeled Residue Count: 852 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tenA homolog/Thi-4 Thiaminase	A, B, C, D	221	Pyrobaculum aerophilum str. IM2	Mutation(s): 0  Gene Names: tena/thi4 (pag5_170) EC: 2.5.1.2
UniProt
Find proteins for Q8ZZM9 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZZM9  Go to UniProtKB:  Q8ZZM9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	E [auth A], G [auth C], I [auth D]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
PO4	H [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.757	α = 90
b = 134.926	β = 90
c = 144.029	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Sawaya, M.R., Chan, S., Han, G.W., Perry, L.J.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary