2G64 | pdb_00002g64

Structure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin synthase

• PDB DOI: https://doi.org/10.2210/pdb2G64/pdb

• Classification: LYASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-24 Released: 2006-03-14 
• Deposition Author(s): Wengerter, B.C., Patskovsky, Y., Zhan, C., Ramagopal, U., Milstein, S., Vidal, M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.333 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Caenorhabditis Elegans 6-Pyruvoyl Tetrahydropterin Synthase

Wengerter, B.C., Patskovsky, Y., Zhan, C., Ramagopal, U., Milstein, S., Vidal, M., Almo, S.C.

To be published.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.26 kDa 
• Atom Count: 1,362 
• Modeled Residue Count: 140 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-pyruvoyl tetrahydrobiopterin synthase	A	140	Caenorhabditis elegans	Mutation(s): 1  Gene Names: B0041.6 EC: 4.2.3.12
UniProt
Find proteins for O02058 (Caenorhabditis elegans) Explore O02058  Go to UniProtKB:  O02058

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.219 (Depositor), 0.333 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.792	α = 90
b = 69.792	β = 90
c = 160.188	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Wengerter, B.C., Patskovsky, Y., Zhan, C., Ramagopal, U., Milstein, S., Vidal, M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description