2P79

Crystal structure of TTHB049 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2P79/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-20 Released: 2007-09-25 
• Deposition Author(s): Sugahara, M., Taketa, M., Kageyama, Y., Matsuura, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Crystal structure of TTHB049 from Thermus thermophilus HB8

Sugahara, M., Taketa, M., Kageyama, Y., Matsuura, Y., Kunishima, N.

To be published.

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: 39.68 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 341 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ribazole-5'-phosphate phosphatase	A, B	177	Thermus thermophilus HB8	Mutation(s): 1  EC: 3.1.3.73
UniProt
Find proteins for Q53WB3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53WB3  Go to UniProtKB:  Q53WB3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.948	α = 90
b = 91.886	β = 90
c = 110.967	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Sugahara, M., Taketa, M., Kageyama, Y., Matsuura, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description