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- PDB-2wde: Termus thermophilus Sulfate thiohydrolase SoxB in complex with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wde | ||||||
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Title | Termus thermophilus Sulfate thiohydrolase SoxB in complex with thiosulfate | ||||||
![]() | SULFUR OXIDATION PROTEIN SOXB | ||||||
![]() | HYDROLASE / SULFUR OXIDATION PATHWAY / SOX / SOXB / SULFUR-SULFUR HYDROLYSIS / CYS S-THIOSULFONATE | ||||||
Function / homology | ![]() nucleotide catabolic process / outer membrane-bounded periplasmic space / hydrolase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sauve, V. / Roversi, P. / Leath, K.J. / Garman, E.F. / Antrobus, R. / Lea, S.M. / Berks, B.C. | ||||||
![]() | ![]() Title: Mechanism for the Hydrolysis of a Sulfur-Sulfur Bond Based on the Crystal Structure of the Thiosulfohydrolase Soxb. Authors: Sauve, V. / Roversi, P. / Leath, K.J. / Garman, E.F. / Antrobus, R. / Lea, S.M. / Berks, B.C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.4 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 277.7 KB | Display | ![]() |
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Full document | ![]() | 408.8 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wdcSC ![]() 2wddC ![]() 2wdfC 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: 62747.434 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-573 Source method: isolated from a genetically manipulated source Details: THERMUS THERMOPHILUS HB27 SOXB / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||||
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#2: Chemical | ChemComp-TBU / #3: Chemical | #4: Chemical | ChemComp-THJ / | #5: Water | ChemComp-HOH / | Nonpolymer details | MANGANESE II ION (MN): SUPPLEMENT | Sequence details | STREP II TAG AT THE NTERMINUS REPLACED THE TAT SIGNAL PEPTIDE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 5MM TRISHCL PH 8.0, 0.1M NACL, 0.05M TRIS-ACETATE PH 8.5, 12-13% T-BUTANOL, 1MM MNCL2 AND 1 MM NA2S2O3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER / Detector: CCD / Details: MONTEL OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→64.2 Å / Num. obs: 48244 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 19.65 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WDC Resolution: 1.85→64.15 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AUTOBUSTER BETA VERSION 2.5.1 DECEMBER 2008
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Displacement parameters | Biso mean: 21.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→64.15 Å
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LS refinement shell | Resolution: 1.85→1.96 Å / Total num. of bins used: 9
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