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Yorodumi- PDB-3aro: Crystal Structure Analysis of Chitinase A from Vibrio harveyi wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aro | ||||||
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Title | Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - apo structure | ||||||
Components | Chitinase AChitinase A N-terminal domain | ||||||
Keywords | HYDROLASE / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.22 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 | 3aro.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aro.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 3aro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/3aro ftp://data.pdbj.org/pub/pdb/validation_reports/ar/3aro | HTTPS FTP |
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-Related structure data
Related structure data | 3arpC 3arqC 3arrC 3arsC 3artC 3aruC 3arvC 3arwC 3arxC 3aryC 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 | ChemComp-GOL / |
#3: 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: 2.4 Å3/Da / Density % sol: 48.74 % |
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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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2009 / Details: helios mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.22→19.822 Å / Num. obs: 28924 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.639 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.22→19.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.1834 / WRfactor Rwork: 0.1237 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8776 / SU B: 5.169 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2754 / SU Rfree: 0.2118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / 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: 80.13 Å2 / Biso mean: 14.1065 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.224→2.281 Å / Total num. of bins used: 20
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