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Yorodumi- PDB-2zvp: Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zvp | ||||||
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Title | Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and p-nitrophenol | ||||||
Components | Tyrosine-ester sulfotransferase | ||||||
Keywords | TRANSFERASE / SULT1D1 / sulfotransferase / p-nitrophenol / sulfonation | ||||||
Function / homology | Function and homology information Transferases; Transferring sulfur-containing groups; Sulfotransferases / aryl sulfotransferase activity / sulfation / sulfotransferase activity / sulfate assimilation / catecholamine metabolic process / lipid metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Structural basis for the broad range substrate specificity of a novel mouse cytosolic sulfotransferase--mSULT1D1 Authors: Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zvp.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zvp.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zvp_validation.pdf.gz | 822.8 KB | Display | wwPDB validaton report |
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Full document | 2zvp_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 2zvp_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 2zvp_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/2zvp ftp://data.pdbj.org/pub/pdb/validation_reports/zv/2zvp | HTTPS FTP |
-Related structure data
Related structure data | 2zvqC 2zptS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35128.293 Da / Num. of mol.: 1 / Fragment: residues 1-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult1d1 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9R2C2, UniProt: Q3UZZ6*PLUS, EC: 2.8.2.9 | ||||
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#2: Chemical | ChemComp-A3P / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 3.1 Å3/Da / Density % sol: 60.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 16% PEG 10000, 10mM dithiothreitol, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 87253 / Num. obs: 87253 / % possible obs: 83 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.301→1.335 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.507 / % possible all: 34.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZPT Resolution: 1.3→23.41 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.705 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / 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: 15.547 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→23.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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