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Yorodumi- PDB-2z6v: Crystal structure of sulfotransferase STF9 from Mycobacterium avium -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6v | ||||||
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Title | Crystal structure of sulfotransferase STF9 from Mycobacterium avium | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / sulfotransferase | ||||||
Function / homology | Sulfotransferase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / PALMITIC ACID / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Mycobacterium avium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hassain, M.M. / Moriizumi, Y. / Tanaka, S. / Kimura, M. / Kakuta, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of sulfotransferase STF9 from Mycobacterium avium Authors: Hassain, M.M. / Moriizumi, Y. / Tanaka, S. / 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 | 2z6v.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6v.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6v_validation.pdf.gz | 749 KB | Display | wwPDB validaton report |
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Full document | 2z6v_full_validation.pdf.gz | 763.5 KB | Display | |
Data in XML | 2z6v_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 2z6v_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6v ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6v | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48118.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (bacteria) / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codonplusRIL / References: UniProt: A0QK82, UniProt: A0A0H2ZS19*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-PLM / |
#4: 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: 3.89 Å3/Da / Density % sol: 68.4 % |
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Crystal grow | Temperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M Magnesium sulfate, 0.1M MES (pH 6.5), 0.15M Sodium choloride, 10mM PAP, 10mM DTT, 50mM Tris-HCl (pH 7.0) , VAPOR DIFFUSION, HANGING DROP, temperature 293.4K |
-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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 23316 / Num. obs: 23316 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.427 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 358232.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4522 Å2 / ksol: 0.361355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→49.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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