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- PDB-2zph: Complex of Fe-type nitrile hydratase with tert-butylisonitrile, p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zph | ||||||
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Title | Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 340min at 293K | ||||||
![]() | (Nitrile hydratase subunit ...) x 2 | ||||||
![]() | LYASE / Iron / Metal-binding / Oxidation | ||||||
Function / homology | ![]() nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hashimoto, K. / Suzuki, H. / Taniguchi, K. / Noguchi, T. / Yohda, M. / Odaka, M. | ||||||
![]() | ![]() Title: Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile Authors: Hashimoto, K. / Suzuki, H. / Taniguchi, K. / Noguchi, T. / 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 | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zpbSC ![]() 2zpeC ![]() 2zpfC ![]() 2zpgC ![]() 2zpiC 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
-Nitrile hydratase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22933.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 23514.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 5 types, 545 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/TB0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TB0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FE / | ||||
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#4: Chemical | ChemComp-TB0 / | ||||
#5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 0.1M Tris-HCl pH 7.5, 300mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→66.519 Å / Num. obs: 59023 / % possible obs: 97.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZPB Resolution: 1.59→7.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.22 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The authors think the intermediate structure between substrate and product; The tert-butyl isocyanide (TB0) substrate binds the metal ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The authors think the intermediate structure between substrate and product; The tert-butyl isocyanide (TB0) substrate binds the metal directly and then a water molecule, which, activated by O delta atom of CSO, makes a nucleophilic attack on the isonitrile carbon to produce tBuNH2 and CO. These atoms may be disordered because the occupancies of oxygen atom of CMO and O delta atom of CSO were converged to 0.30 and 0.70 respectively. When a water molecule, which, activated by O delta atom of CSO, comes close to the substrate, kicks the O delta atom out of the active center.
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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: 13.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.63 Å / Total num. of bins used: 20
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