+Open data
-Basic information
Entry | Database: PDB / ID: 1zd1 | ||||||
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Title | Human Sulfortransferase SULT4A1 | ||||||
Components | Sulfotransferase 4A1 | ||||||
Keywords | TRANSFERASE / SGC / SULT4A1 / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information Transferases; Transferring sulfur-containing groups; Sulfotransferases / Cytosolic sulfonation of small molecules / sulfation / sulfotransferase activity / steroid metabolic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Dong, A. / Dombrovski, L. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Sundstrom, M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos Biol. / Year: 2007 Title: Structural and chemical profiling of the human cytosolic sulfotransferases. Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, ...Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Vedadi, M. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zd1.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zd1.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zd1_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 1zd1_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1zd1_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 1zd1_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zd1 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zd1 | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 33124.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SULT4A1, SULTX3 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9BR01, Transferases; Transferring sulfur-containing groups; Sulfotransferases #2: Chemical | ChemComp-GOL / | #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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6.5 Details: 20% PEG3350, 0.2M Ammonium Tartrate, VAPOR DIFFUSION, temperature 300K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 23, 2005 / Details: VeriMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→82 Å / Num. obs: 28728 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.87 / Rsym value: 0.87 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.55 / Rsym value: 0.6 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→82.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.542 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.239 / 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: 37.437 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.24→82.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.237→2.295 Å / Total num. of bins used: 20
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