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- PDB-3a8o: Crystal structure of Nitrile Hydratase complexed with Trimethylac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a8o | ||||||
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Title | Crystal structure of Nitrile Hydratase complexed with Trimethylacetamide | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamanaka, Y. / Hashimoto, K. / Ohtaki, A. / Noguchi, K. / Yohda, M. / Odaka, M. | ||||||
![]() | ![]() Title: Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase Authors: Yamanaka, Y. / Hashimoto, K. / Ohtaki, A. / Noguchi, K. / Yohda, M. / Odaka, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a8gC ![]() 3a8hC ![]() 3a8lC ![]() 3a8mC ![]() 2ahjS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 23065.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 23514.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-FE / ![]() |
#4: Chemical | ChemComp-TAY / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow![]() | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.46→50 Å / Num. obs: 71422 / % possible obs: 93.3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2ahj Resolution: 1.47→27.51 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.196 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.084 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.674 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→27.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.468→1.506 Å / Total num. of bins used: 20
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