3D7J

SCO6650, a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb3D7J/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-21 Released: 2008-10-21 
• Deposition Author(s): Spoonamore, J.E., Roberts, S.A., Heroux, A., Bandarian, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.224 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor.

Spoonamore, J.E., Roberts, S.A., Heroux, A., Bandarian, V.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 875-879

• PubMed: 18931427 
• DOI: https://doi.org/10.1107/S1744309108027048
• Primary Citation of Related Structures:  
  3D7J


• PubMed Abstract: 
  

  The X-ray crystal structure of the 6-pyruvoyltetrahydropterin synthase (PTPS) homolog from Streptomyces coelicolor, SCO 6650, was solved at 1.5 A resolution. SCO 6650 forms a hexameric T-fold that closely resembles other PTPS proteins. The biological activity of SCO 6650 is unknown, but it lacks both a required active-site zinc metal ion and the essential catalytic triad and does not catalyze the PTPS reaction. However, SCO 6650 maintains active-site residues consistent with binding a pterin-like substrate.

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Organizational Affiliation: 

Department of Biochemistry, University of Arizona, Tucson, AZ 85721, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 100.26 kDa 
• Atom Count: 7,026 
• Modelled Residue Count: 806 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein SCO6650	A, B, C, D, E, F	152	Streptomyces coelicolor	Mutation(s): 0  Gene Names: SCO6650 EC: 4.1.2.50
UniProt
Find proteins for O86696 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore O86696  Go to UniProtKB:  O86696

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	I [auth A], J [auth B], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.224 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.4	α = 90
b = 88	β = 90
c = 120.9	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Spoonamore, J.E., Roberts, S.A., Heroux, A., Bandarian, V.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-28
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary