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- PDB-3fs5: Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog ... -

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Basic information

Entry
Database: PDB / ID: 3fs5
TitleCrystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain
ComponentsUncharacterized protein YGR203W
KeywordsTRANSFERASE / rhodanese family
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / dephosphorylation / protein tyrosine phosphatase activity / nucleus / cytoplasm
Similarity search - Function
Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CDC25-like phosphatase YCH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsYeo, H.K. / Lee, J.Y.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain
Authors: Yeo, H.K. / Lee, J.Y.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YGR203W


Theoretical massNumber of molelcules
Total (without water)17,6341
Polymers17,6341
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.482, 50.954, 91.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein YGR203W


Mass: 17633.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YGR203W / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P42937
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.0 - 1.4M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 1, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 14393 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.205 1344 RANDOM
Rwork0.182 --
obs-12955 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 0 90 1323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.01
X-RAY DIFFRACTIONc_bond_d0.005

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