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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.229 (Depositor), 0.225 (DCC)
R-Value Work:
0.207 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YGA

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Yeast Aldose_1_Epimerase

Patskovsky, Y., Almo, S.C.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53757
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229 (Depositor), 0.225 (DCC)
R-Value Work: 0.207 (Depositor), 0.205 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-01-18

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.