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- PDB-2zyw: crystal structure of mouse cytosolic sulfotransferase mSULT1D1 co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zyw | ||||||
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Title | crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and p-nitrophenol, obtained by two-step soaking method | ||||||
![]() | Tyrosine-ester sulfotransferase | ||||||
![]() | TRANSFERASE / SULT1D1 / SULT / sulfotransferase / PAP / p-nitrophenol / sulfonation | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y. | ||||||
![]() | ![]() Title: Snapshot of a Michaelis complex in a sulfuryl transfer reaction: Crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter substrate Authors: Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zytC ![]() 2zyuC ![]() 2zyvC ![]() 2zptS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q9R2C2, UniProt: Q3UZZ6*PLUS, EC: 2.8.2.9 | ||||
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#2: Chemical | ChemComp-A3P / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 16% PEG 10000, 10mM DTT, 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: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 39743 / Num. obs: 39743 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3966 / Rsym value: 0.387 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZPT Resolution: 1.8→26.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.941 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.096 / 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: 24.162 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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