+Open data
-Basic information
Entry | Database: PDB / ID: 6jm7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Ostrinia furnacalis Group IV chitinase | ||||||
Components | ofchtiv | ||||||
Keywords | HYDROLASE / chitinase / Ostrinia furnacalis / group IV | ||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Ostrinia furnacalis (Asian corn borer) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.572 Å | ||||||
Authors | Liu, T. / Yang, Q. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Insect Biochem.Mol.Biol. / Year: 2020 Title: Structure and property of group IV insect chitinase, a potential drug target and biopesticide Authors: Liu, T. / Guo, X. / Bu, Y. / Zhou, Y. / Duan, Y. / Yang, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jm7.cif.gz | 94 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jm7.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jm7_validation.pdf.gz | 412.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jm7_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 6jm7_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6jm7_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/6jm7 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/6jm7 | HTTPS FTP |
-Related structure data
Related structure data | 6jm8C 6jmbC 5wupS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43943.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Plasmid: pPIC9k / Production host: Pichia (fungus) / Strain (production host): GS115 / References: UniProt: A0A482LWB1*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 1600 mM sodium phosphate monobasic, 400 mM potassium phosphate dibasic, 100 mM sodium phosphate dibasic, 100 mM citric acid, pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97778 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 56099 / % possible obs: 99.8 % / Redundancy: 9.8 % / Rsym value: 0.075 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 5.45 / Num. unique obs: 2729 / Rsym value: 1.049 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5wup Resolution: 1.572→35.797 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.76
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.572→35.797 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|