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Yorodumi- PDB-3aay: Crystal structure of probable thiosulfate sulfurtransferase CYSA3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aay | ||||||
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Title | Crystal structure of probable thiosulfate sulfurtransferase CYSA3 (RV3117) from Mycobacterium tuberculosis: orthorhombic form | ||||||
Components | Putative thiosulfate sulfurtransferase | ||||||
Keywords | TRANSFERASE / M. tuberculosis / sulfurtranserase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium (TBSGC) | ||||||
Function / homology | Function and homology information thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / peptidoglycan-based cell wall / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sankaranarayanan, R. / Witholt, S.J. / Cherney, M.M. / Garen, C.R. / Cherney, L.T. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of probable thiosulfate sulfurtransferase CysA3 (Rv3117) from Mycobacterium tuberculosis Authors: Sankaranarayanan, R. / Witholt, S.J. / Cherney, M.M. / Garen, C.R. / Cherney, L.T. / James, M.N.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Expression, purification, crystallization and preliminary X-ray analysis of Rv3117, a probable thiosulfate sulfurtransferase (CysA3) from Mycobacterium tuberculosis Authors: Witholt, S.J. / Sankaranarayanan, R. / Garen, C.R. / Cherney, M.M. / Cherney, L.T. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aay.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aay.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 3aay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aay_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 3aay_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 3aay_validation.xml.gz | 27 KB | Display | |
Data in CIF | 3aay_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/3aay ftp://data.pdbj.org/pub/pdb/validation_reports/aa/3aay | HTTPS FTP |
-Related structure data
Related structure data | 3aaxC 1uarS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 31068.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: CysA3 / Plasmid: pDEST-17 / Production host: Escherichia coli (E. coli) References: UniProt: O05793, UniProt: P9WHF9*PLUS, thiosulfate sulfurtransferase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein Concentration 8 mg/ml in Tris Buffer pH 7.5, Precipitant 0.1M Bis-Tris at pH 5.5, 3% MPD, 5mM sodium thiosulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976067 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2008 Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976067 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 47968 / Num. obs: 47968 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4717 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UAR Resolution: 1.9→37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.259 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE ELECTRON DENSITY FOR THE RESIDUES 176-180 IN CHAIN A IS NOT RESOLVED. HENCE, THESE RESIDUES WERE NOT MODELLED.
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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: 25.376 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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