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- PDB-1yga: CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW Y... -

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Basic information

Entry
Database: PDB / ID: 1yga
TitleCRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
ComponentsHypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region
KeywordsISOMERASE / ALDOSE_1_EPIMERASE / SUGAR METABOLISM / PREDICTED / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Isomerases / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / glucose metabolic process / carbohydrate binding
Similarity search - Function
Aldose 1-epimerase, conserved site / Aldose 1-epimerase putative active site. / : / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized isomerase YNR071C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsPatskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of the Yeast Aldose_1_Epimerase
Authors: Patskovsky, Y. / Almo, S.C.
History
DepositionJan 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region
B: Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region


Theoretical massNumber of molelcules
Total (without water)75,7932
Polymers75,7932
Non-polymers00
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-12 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.860, 88.070, 103.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer composed of two identical monomers. The dimeric structure is stabilized by intra-chain S-S bridges. The asymmetric unit contains dimer.

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Components

#1: Protein Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region


Mass: 37896.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YN9A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53757, aldose 1-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS-HCL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 44056 / Num. obs: 44056 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.077 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2328 / Rsym value: 0.25 / % possible all: 48.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 242583.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1320 3 %RANDOM
Rwork0.207 ---
all0.23 44056 --
obs0.207 43705 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.0966 Å2 / ksol: 0.324547 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.89 Å20 Å20 Å2
2--5.66 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 0 539 5783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it1.972.5
X-RAY DIFFRACTIONc_mcangle_it2.83
X-RAY DIFFRACTIONc_scbond_it2.943
X-RAY DIFFRACTIONc_scangle_it4.144
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 120 2.8 %
Rwork0.28 4112 -
obs-4112 52.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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