+Open data
-Basic information
Entry | Database: PDB / ID: 2z5f | |||||||||
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Title | Human sulfotransferase Sult1b1 in complex with PAP | |||||||||
Components | Sulfotransferase family cytosolic 1B member 1 | |||||||||
Keywords | TRANSFERASE / SULT / SULFOTRANSFERASE / PAP / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | Function and homology information phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / ethanol catabolic process / sulfation ...phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / ethanol catabolic process / sulfation / sulfotransferase activity / epithelial cell differentiation / xenobiotic metabolic process / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Dombrovski, L. / Pegasova, T. / Wu, H. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structures of human sulfotransferases SULT1B1 and SULT1C1 complexed with the cofactor product adenosine-3'-5'-diphosphate (PAP) Authors: Dombrovski, L. / Dong, A. / Bochkarev, A. / Plotnikov, A.N. | |||||||||
History |
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Remark 999 | SEQUENCE Lys183 is mutated to Arg183 as result of unintentional PCR-generated mutation. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z5f.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z5f.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/2z5f ftp://data.pdbj.org/pub/pdb/validation_reports/z5/2z5f | HTTPS FTP |
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-Related structure data
Related structure data | 3bfxC 1g3mS 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: 35121.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1B1 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL References: UniProt: O43704, Transferases; Transferring sulfur-containing groups; Sulfotransferases #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: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BisTris, 0.2M ammonium sulfate, 16-20% polyethylene glycol 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 24, 2004 / Details: OSMIC |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 37990 / Num. obs: 37990 / % possible obs: 96.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G3M Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.706 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.199 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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