+Open data
-Basic information
Entry | Database: PDB / ID: 4gra | ||||||
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Title | Crystal structure of SULT1A1 bound with PAP | ||||||
Components | Sulfotransferase 1A1 | ||||||
Keywords | TRANSFERASE / sulfotransferase / estradiol / hormone regulation | ||||||
Function / homology | Function and homology information aryl sulfotransferase / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...aryl sulfotransferase / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / catecholamine metabolic process / Paracetamol ADME / amine metabolic process / estrogen metabolic process / xenobiotic metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Kim, J. / Cook, I. / Wang, T. / Falany, C.N. / Leyh, T.S. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The gate that governs sulfotransferase selectivity. Authors: Cook, I. / Wang, T. / Almo, S.C. / Kim, J. / Falany, C.N. / Leyh, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gra.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gra.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4gra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4gra ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4gra | HTTPS FTP |
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-Related structure data
Related structure data | 2d06S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34644.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1A1, STP, STP1, OK/SW-cl.88 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P50225, aryl sulfotransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris PH 8.0, 20% PEG, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2011 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. obs: 20267 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2D06 Resolution: 2.56→48.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.461 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 35.669 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→48.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.564→2.63 Å / Total num. of bins used: 20
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