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- PDB-2zcf: Mutational study on Alpha-Gln90 of Fe-type nitrile hydratase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zcf | ||||||
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Title | Mutational study on Alpha-Gln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771 | ||||||
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![]() | LYASE / CYSTEINE-SULFINIC ACID / CYSTEINE-SULFENIC ACID / PHOTO-REACTIVE / NITRILE / HYDRATION / PHOTO-ACTIVATION / Iron / Metal-binding / Oxidation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takarada, H. / Kawano, Y. / Hashimoto, K. / Nakayama, H. / Ueda, S. / Yohda, M. / Kamiya, N. / Dohmae, N. / Maeda, M. / Odaka, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771 Authors: Takarada, H. / Kawano, Y. / Hashimoto, K. / Nakayama, H. / Ueda, S. / Yohda, M. / Kamiya, N. / Dohmae, N. / Maeda, 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 | ![]() | 111.6 KB | Display | ![]() |
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PDB format | ![]() | 82.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ahjS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis: -x+2,y,-z |
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Components
#1: Protein | Mass: 22919.848 Da / Num. of mol.: 1 / Mutation: Q90N 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-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, MAGNESIUM CHLORIDE, 50mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2004 / Details: Pt |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. all: 85342 / Num. obs: 85342 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.43→1.48 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.48 / % possible all: 77.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AHJ Resolution: 1.43→8 Å / Num. parameters: 15501 / Num. restraintsaints: 13344 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3865.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→8 Å
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Refine LS restraints |
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