+Open data
-Basic information
Entry | Database: PDB / ID: 1wvv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of chitinase C mutant E147Q | ||||||
Components | chitinase C | ||||||
Keywords | HYDROLASE / family 19 chitinase / whole structure | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å | ||||||
Authors | Kezuka, Y. / Watanabe, T. / Nonaka, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Studies of a Two-domain Chitinase from Streptomyces griseus HUT6037 Authors: Kezuka, Y. / Ohishi, M. / Itoh, Y. / Watanabe, J. / Mitsutomi, M. / Watanabe, T. / Nonaka, T. #1: Journal: Biosci.Biotechnol.Biochem. / Year: 2002 Title: Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function Authors: Itoh, Y. / Kawase, T. / Nikaidou, N. / Fukada, H. / Mitsutomi, M. / Watanabe, T. / Itoh, Y. #2: Journal: Microbiology / Year: 1999 Title: Family 19 chitinases of Streptomyces species: characterization and distribution Authors: Watanabe, T. / Kanai, R. / Kawase, T. / Tanabe, T. / Mitsutomi, M. / Sakuda, S. / Miyashita, K. #3: Journal: J.Bacteriol. / Year: 1996 Title: A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037 Authors: Ohno, T. / Armand, S. / Hata, T. / Nikaidou, N. / Henrissat, B. / Mitsutomi, M. / Watanabe, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wvv.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wvv.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvv ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28496.182 Da / Num. of mol.: 2 / Fragment: residues 30-294 / Mutation: E147Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Plasmid: pET12a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 2662299, UniProt: O50152*PLUS, chitinase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Sodium chloride, Sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003 |
Radiation | Monochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→56.79 Å / Num. all: 47236 / Num. obs: 47236 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.9 % / Biso Wilson estimate: 30.337 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3 / Num. unique all: 3466 / Rsym value: 0.242 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2→56.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.693 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.12 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.077 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→56.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|