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- PDB-6xgt: Crystal structure of cyanase from the thermophilic fungus Thermom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xgt | ||||||
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Title | Crystal structure of cyanase from the thermophilic fungus Thermomyces lanuginosus | ||||||
![]() | Cyanate hydratase | ||||||
![]() | HYDROLASE / cyanase | ||||||
Function / homology | FORMIC ACID / MALONATE ION![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Choi, P.H. / Ranjan, B. / Tong, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a thermophilic fungal cyanase and its implications on the catalytic mechanism for bioremediation. Authors: Ranjan, B. / Choi, P.H. / Pillai, S. / Permaul, K. / Tong, L. / Singh, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.7 KB | Display | ![]() |
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PDB format | ![]() | 268.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 524.7 KB | Display | ![]() |
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Full document | ![]() | 539 KB | Display | |
Data in XML | ![]() | 64.3 KB | Display | |
Data in CIF | ![]() | 90.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dw9S 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
#1: Protein | Mass: 20113.863 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2% (w/v) Tacsimate (pH 8.0), 0.1 M Tris (pH 8.5), and 16% (w/v) polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 99692 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.381 / Num. unique obs: 9819 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dw9 Resolution: 2.2→45.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.541 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.17 / 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: 25.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→45.36 Å
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Refine LS restraints |
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