+Open data
-Basic information
Entry | Database: PDB / ID: 3vyg | ||||||
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Title | Crystal structure of Thiocyanate hydrolase mutant R136W | ||||||
Components | (Thiocyanate hydrolase subunit ...) x 3 | ||||||
Keywords | HYDROLASE / Thiocyanate hydrolase / Cysteine-sulfenic acid / Cysteine-sulfic acid / metalloenzyme | ||||||
Function / homology | Function and homology information thiocyanate hydrolase / thiocyanate hydrolase activity / thiocyanate catabolic process / transition metal ion binding Similarity search - Function | ||||||
Biological species | Thiobacillus thioparus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Yamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M. | ||||||
Citation | Journal: To be published Title: Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase Authors: Yamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vyg.cif.gz | 427.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vyg.ent.gz | 346.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vyg_validation.pdf.gz | 527.6 KB | Display | wwPDB validaton report |
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Full document | 3vyg_full_validation.pdf.gz | 565.7 KB | Display | |
Data in XML | 3vyg_validation.xml.gz | 87.8 KB | Display | |
Data in CIF | 3vyg_validation.cif.gz | 127.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyg ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyg | HTTPS FTP |
-Related structure data
Related structure data | 3vyhC 2dd5S C: citing same article (ref.) S: Starting model for refinement |
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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
-Thiocyanate hydrolase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 14507.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Gene: scnA / Production host: Escherichia coli (E. coli) / References: UniProt: O66187, thiocyanate hydrolase #2: Protein | Mass: 18065.549 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Gene: scnB / Production host: Escherichia coli (E. coli) / References: UniProt: O66186, thiocyanate hydrolase #3: Protein | Mass: 27648.445 Da / Num. of mol.: 4 / Mutation: R136W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Gene: scnC / Production host: Escherichia coli (E. coli) / References: UniProt: O66188, thiocyanate hydrolase |
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-Non-polymers , 3 types, 1508 molecules
#4: Chemical | ChemComp-3CO / #5: Chemical | ChemComp-TLA / #6: 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: 3.5 Å3/Da / Density % sol: 64.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M potassium phosphate pH 6.8, 1.4M potassium phosphate tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. all: 343322 / Num. obs: 325674 / % possible obs: 96.5 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.72→1.78 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 9.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DD5 Resolution: 1.72→33.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.626 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→33.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.721→1.766 Å / Total num. of bins used: 20
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