[English] 日本語
Yorodumi- PDB-3g6l: The crystal structure of a chitinase CrChi1 from the nematophagou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g6l | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a chitinase CrChi1 from the nematophagous fungus Clonostachys rosea | ||||||
Components | Chitinase | ||||||
Keywords | HYDROLASE / chitinase CrChi1 / nematophagous fungus / Clonostachys rosea / Glycosidase | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bionectria ochroleuca (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gan, Z. / Lou, Z. / Rao, Z. / Zhang, K.-Q. | ||||||
Citation | Journal: Microbiology / Year: 2010 Title: Crystal structure and mutagenesis analysis of chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with the inhibitor caffeine Authors: Yang, J. / Gan, Z. / Lou, Z. / Tao, N. / Mi, Q. / Liang, L. / Sun, Y. / Guo, Y. / Huang, X. / Zou, C. / Rao, Z. / Meng, Z. / Zhang, K.-Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g6l.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g6l.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g6l_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3g6l_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 3g6l_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3g6l_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g6l ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g6l | HTTPS FTP |
-Related structure data
Related structure data | 3g6mC 1w9pS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44045.773 Da / Num. of mol.: 1 / Fragment: residues 21-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bionectria ochroleuca (fungus) / Description: synonym is Clonostachys rosea / Gene: Crchi1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A9LI60, chitinase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M ammonium dihydrogen phosphate, 15%(w/v) PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 6, 2008 / Details: osmic mirror |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 34080 / Num. obs: 30889 / % possible obs: 95 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.48 / % possible all: 92.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W9P Resolution: 1.8→45.59 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.51 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.537 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|