2DTT | pdb_00002dtt

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3 complexed with (1'R,2'S)-biopterin

• PDB DOI: https://doi.org/10.2210/pdb2DTT/pdb

• Classification: LYASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-15 Released: 2007-01-15 
• Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3

Bagautdinov, B., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.64 kDa 
• Atom Count: 5,910 
• Modeled Residue Count: 649 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0634	A, B, C, D, E, F	115	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0634
UniProt
Find proteins for O58368 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58368  Go to UniProtKB:  O58368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H4B	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.682	α = 90
b = 105.445	β = 90.95
c = 96.147	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-15 
Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description