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Yorodumi- PDB-1h4m: Sulfurtransferase from Azotobacter vinelandii in complex with pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h4m | ||||||
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Title | Sulfurtransferase from Azotobacter vinelandii in complex with phosphate | ||||||
Components | PUTATIVE THIOSULFATE SULFURTRANSFERASERhodanese | ||||||
Keywords | TRANSFERASE / SULFUR METABOLISM / THIOSULFATE:CYANIDE | ||||||
Function / homology | Function and homology information thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | AZOTOBACTER VINELANDII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bordo, D. / Forlani, F. / Spallarossa, A. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M. | ||||||
Citation | Journal: Biol.Chem. / Year: 2001 Title: A Persulfurated Cysteine Promotes Active Site Reactivity in Azotobacter Vinelandii Rhodanse Authors: Bordo, D. / Forlani, F. / Spallarossa, A. / Colnaghi, R. / Carpen, A. / Bolognesi, M. / Pagani, S. #1: Journal: J.Mol.Biol. / Year: 2000 Title: The Crystal Structure of a Sulfurtransferase from Azotobacter Vinelandii Highliths the Evolutionary Relationship between the Rhodanese and Phosphatase Enzyme Families Authors: Bordo, D. / Deriu, D. / Colnaghi, R. / Carpen, A. / Pagani, S. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h4m.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4m.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4m ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4m | HTTPS FTP |
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-Related structure data
Related structure data | 1h4kC 1e0cS 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: 29664.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Cellular location: CYTOPLASM / Gene: RHDA / Plasmid: PQE32 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI M15 (bacteria) / Variant (production host): PRE4 / References: UniProt: P52197, thiosulfate sulfurtransferase | ||
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#2: Chemical | #3: 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 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 6.5 Details: 1.7 M MGSO4, 50 MM MES PH 6.0, 5% (V/V)ETHANEDIOL. NATIVE RHDA CRYSTALS SOAKED IN 5 MM AMMONIUM HYDROGEN PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8349 |
Detector | Type: MARRESEARCH |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8349 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.2 Å / Num. obs: 15806 / % possible obs: 73.7 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 24 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E0C Resolution: 2.1→20 Å / SU B: 4.77755 / SU ML: 0.13366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22665 / Details: NONE
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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