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Open data
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Basic information
Entry | Database: PDB / ID: 3wuy | ||||||
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Title | Crystal structure of Nit6803 | ||||||
![]() | Nitrilase | ||||||
![]() | HYDROLASE / Nitrilase | ||||||
Function / homology | ![]() : / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yuan, Y.A. / Yin, B. / Wang, C. | ||||||
![]() | ![]() Title: Structural insights into enzymatic activity and substrate specificity determination by a single amino acid in nitrilase from Syechocystis sp. PCC6803 Authors: Zhang, L. / Yin, B. / Wang, C. / Jiang, S. / Wang, H. / Yuan, Y.A. / Wei, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.7 KB | Display | ![]() |
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PDB format | ![]() | 188.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.5 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 6 - 290 / Label seq-ID: 9 - 293
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Components
#1: Protein | Mass: 38306.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Sodium Cacodylate, PEG4K, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2012 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 20270 / Num. obs: 20231 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.1→3.18 Å / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Structure determined by MAD and refinement using the native data. Resolution: 3.1→49.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 24.022 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.69 / ESU R Free: 0.284 / 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: 63.374 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→49.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 17181 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.099→3.18 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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