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- PDB-3wh1: Crystal Structure of a Family GH19 Chitinase from Bryum coronatum... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wh1 | |||||||||
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Title | Crystal Structure of a Family GH19 Chitinase from Bryum coronatum in complex with (GlcNAc)4 at 1.0 A resolution | |||||||||
![]() | Chitinase A | |||||||||
![]() | HYDROLASE / Chitinase / Carbohydrate | |||||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Numata, T. / Umemoto, N. / Ohnuma, T. / Fukamizo, T. | |||||||||
![]() | ![]() Title: Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. Authors: Ohnuma, T. / Umemoto, N. / Nagata, T. / Shinya, S. / Numata, T. / Taira, T. / Fukamizo, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.5 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.8 KB | Display | ![]() |
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Full document | ![]() | 775.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ij4SC 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
#1: Protein | Mass: 22738.990 Da / Num. of mol.: 1 / Fragment: UNP residues 24-228 / Mutation: E61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.09M Tris-HCl(pH 8.5), 1.35M di-Ammonium hydrogen phosphate, 0.001M CoCl2, 0.01M Sodium acetate(pH 4.6), 0.1M 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromater, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 98800 / % possible obs: 98.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 33.25 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.13 / Num. unique all: 30901 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4IJ4 Resolution: 1→44.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.473 / SU ML: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.163 Å2
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Refinement step | Cycle: LAST / Resolution: 1→44.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.999→1.025 Å / Total num. of bins used: 20
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