1YGA | pdb_00001yga

CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

• PDB DOI: https://doi.org/10.2210/pdb1YGA/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-04 Released: 2005-01-18 
• Deposition Author(s): Patskovsky, Y., 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: 2.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal Structure of the Yeast Aldose_1_Epimerase

Patskovsky, Y., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 75.79 kDa 
• Atom Count: 5,783 
• Modeled Residue Count: 672 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region	A, B	342	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YN9A EC: 5.1.3.3 (PDB Primary Data), 5 (UniProt)
UniProt
Find proteins for P53757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53757  Go to UniProtKB:  P53757

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.86	α = 90
b = 88.07	β = 90
c = 103.08	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
ARP/wARP	model building
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary