+Open data
-Basic information
Entry | Database: PDB / ID: 2eg3 | ||||||
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Title | Crystal Structure of Probable Thiosulfate Sulfurtransferase | ||||||
Components | Probable thiosulfate sulfurtransferase | ||||||
Keywords | TRANSFERASE / sulfurtransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Sakai, H. / Ebihara, A. / Kitamura, Y. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Probable Thiosulfate Sulfurtransferase Authors: Sakai, H. / Ebihara, A. / Kitamura, Y. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eg3.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eg3.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2eg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/2eg3 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2eg3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25626.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SHV8, Transferases; Transferring sulfur-containing groups; Sulfurtransferases #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6M AMMONIUM SULFATE, 0.1M HEPES BUFFER, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 2, 2005 / Details: monochromator |
Radiation | 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. obs: 51337 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 6.3 / Num. unique all: 5058 / Rsym value: 0.381 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→48.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 534167.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1319 Å2 / ksol: 0.343972 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→48.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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