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Yorodumi- PDB-3ary: Crystal Structure Analysis of Chitinase A from Vibrio harveyi wit... -
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-Basic information
Entry | Database: PDB / ID: 3ary | ||||||
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Title | Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with 2-(imidazolin-2-yl)-5-isothiocyanatobenzofuran | ||||||
Components | Chitinase A | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Vibrio harveyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms Authors: Pantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W. #1: Journal: J.Struct.Biol. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ary.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ary.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ary.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ary_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 3ary_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 3ary_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 3ary_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/3ary ftp://data.pdbj.org/pub/pdb/validation_reports/ar/3ary | HTTPS FTP |
-Related structure data
Related structure data | 3aroC 3arpC 3arqC 3arrC 3arsC 3artC 3aruC 3arvC 3arwC 3arxC 3arzC 3as0C 3as1C 3as2C 3as3C 3b9aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Vibrio harveyi (bacteria) / Strain: LMG7890 / Gene: CHIA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AMP1, chitinase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→19.972 Å / Num. obs: 129106 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.103 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3b9a Resolution: 1.35→19.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1563 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8749 / SU B: 0.935 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0533 / SU Rfree: 0.0573 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.057 / 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: 93 Å2 / Biso mean: 18.0873 Å2 / Biso min: 4.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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