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- PDB-6jav: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jav | ||||||
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Title | Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a piperidine-thienopyridine derivative | ||||||
![]() | Group II chitinase | ||||||
![]() | HYDROLASE / inhibitor complex / chitinase | ||||||
Function / homology | ![]() chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, W. / Zhou, Y. / Yang, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition. Authors: Chen, W. / Zhou, Y. / Yang, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 725.7 KB | Display | ![]() |
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Full document | ![]() | 728.6 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jawC ![]() 6jaxC ![]() 6jayC ![]() 5y29S 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: 44468.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-BC0 / |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Sequence details | The residues 1863-1878 (GDKWDSPREQWRKDAN) seriously influenced its expression and crystallization, ...The residues 1863-1878 (GDKWDSPREQ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium chloride, 0.1M Tris (pH 8.5) and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.437→50 Å / Num. obs: 139584 / % possible obs: 100 % / Redundancy: 16.5 % / Rsym value: 0.103 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.437→1.46 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.37 / Num. unique obs: 4208 / Rsym value: 1.626 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Y29 Resolution: 1.437→27.359 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.14 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.437→27.359 Å
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Refine LS restraints |
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LS refinement shell |
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