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Open data
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Basic information
Entry | Database: PDB / ID: 8hrf | ||||||
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Title | Catalytic domain of Vibrio parahaemolyticus chitinase 1 | ||||||
![]() | Chitinase | ||||||
![]() | HYDROLASE / Chitinase | ||||||
Function / homology | ACETATE ION / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakamura, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytic domain of Vibrio parahaemolyticus chitinase 1 Authors: Nakamura, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.8 KB | Display | ![]() |
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PDB format | ![]() | 192.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.8 KB | Display | ![]() |
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Full document | ![]() | 480.5 KB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 72.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components
#1: Protein | Mass: 61976.609 Da / Num. of mol.: 2 / Fragment: GH18 catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG 8000, 100 mM CaAc2, 100 mM Na-cacodylate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.7 Å / Num. obs: 39898 / % possible obs: 98.75 % / Redundancy: 7.2 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.63 / Num. unique obs: 3994 / % possible all: 97.42 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.7 Å
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Refine LS restraints |
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LS refinement shell |
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