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Yorodumi- PDB-3d1p: Atomic resolution structure of uncharacterized protein from Sacch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d1p | ||||||
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Title | Atomic resolution structure of uncharacterized protein from Saccharomyces cerevisiae | ||||||
Components | Putative thiosulfate sulfurtransferase YOR285W | ||||||
Keywords | TRANSFERASE / atomic structure / atomic resolution structure / PSI / MCSG / mitochondrial rhodanese-like protein / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Mitochondrion | ||||||
Function / homology | Function and homology information Transferases; Transferring sulfur-containing groups; Sulfurtransferases / thiosulfate sulfurtransferase activity / mitochondrial outer membrane / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å | ||||||
Authors | Nocek, B. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Atomic resolution structure of uncharacterized protein from Saccharomyces cerevisiae. Authors: Nocek, B. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d1p.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d1p.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 3d1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/3d1p ftp://data.pdbj.org/pub/pdb/validation_reports/d1/3d1p | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 15619.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / FY1679 / Gene: YOR285W / Plasmid: Modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12305, thiosulfate sulfurtransferase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 2.4 M Ammonium sulfate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6525 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2008 / Details: Mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6525 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→40 Å / Num. all: 60827 / Num. obs: 59810 / % possible obs: 98.3 % / Observed criterion σ(I): 1.8 / Redundancy: 3.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20 |
Reflection shell | Resolution: 0.98→1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2868 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.98→30 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.528 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.817 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1.02 Å / Total num. of bins used: 20
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