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- PDB-3arx: Crystal Structure Analysis of Chitinase A from Vibrio harveyi wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3arx | ||||||
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Title | Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with Propentofylline | ||||||
![]() | Chitinase A | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W. | ||||||
![]() | ![]() Title: Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms Authors: Pantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W. #1: ![]() Title: Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism Authors: Songsiriritthigul, C. / Pantoom, S. / Aguda, A.H. / Robinson, R.C. / Suginta, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.6 KB | Display | ![]() |
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PDB format | ![]() | 121.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aroC ![]() 3arpC ![]() 3arqC ![]() 3arrC ![]() 3arsC ![]() 3artC ![]() 3aruC ![]() 3arvC ![]() 3arwC ![]() 3aryC ![]() 3arzC ![]() 3as0C ![]() 3as1C ![]() 3as2C ![]() 3as3C ![]() 3b9aS 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: 63841.770 Da / Num. of mol.: 1 / Fragment: residues 22-597 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop / pH: 5.6 Details: 16%(W/V) PEG 4000, 21%(v/v) propanol, 0.1M Na-Acetate, pH 5.6, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→40.656 Å / Num. obs: 204668 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.495 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3b9a Resolution: 1.16→40.656 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1852 / WRfactor Rwork: 0.1606 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8915 / SU B: 0.523 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0349 / SU Rfree: 0.0378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 100.51 Å2 / Biso mean: 17.4306 Å2 / Biso min: 4.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→40.656 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.19 Å / Total num. of bins used: 20
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