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- PDB-4mnm: Crystal Structure of GH18 Chitinase (G77W/E119Q mutant) from Cyca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mnm | ||||||
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Title | Crystal Structure of GH18 Chitinase (G77W/E119Q mutant) from Cycas revoluta in complex with (GlcNAc)4 | ||||||
![]() | Chitinase A | ||||||
![]() | HYDROLASE / Chitinase / Carbohydrate | ||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Umemoto, N. / Numata, T. / Ohnuma, T. / Osawa, T. / Taira, T. / Fukamizo, T. | ||||||
![]() | ![]() Title: Crystal Structure of GH18 Chitinase from Cycad, Cycas revoluta Authors: Umemoto, N. / Numata, T. / Ohnuma, T. / Osawa, 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 | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.7 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mnjC ![]() 4mnkC ![]() 3alfS C: citing same article ( 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
#1: Protein | Mass: 38728.621 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-370 / Mutation: G77W, E119Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-EDO / | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.01M Magnesium sulfate heptahydrate, 0.05M Sodium cacodylate trihydrate pH 6.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, 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: 1.8→51.61 Å / Num. obs: 30778 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 43.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 10.6 / Num. unique all: 10829 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ALF Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.532 / SU ML: 0.081 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.127 / 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: 14.451 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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