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Yorodumi- PDB-3b9a: Crystal structure of Vibrio harveyi chitinase A complexed with he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9a | |||||||||
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Title | Crystal structure of Vibrio harveyi chitinase A complexed with hexasaccharide | |||||||||
Components | Chitinase AChitinase A N-terminal domain | |||||||||
Keywords | HYDROLASE / TIM-barrel / Hexasaccharide 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: 1.8 Å | |||||||||
Authors | Songsiriritthigul, C. / Pantoom, S. / Aguda, A.H. / Robinson, R.C. / Suginta, W. | |||||||||
Citation | 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 | 3b9a.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9a.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 3b9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9a ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9a | HTTPS FTP |
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-Related structure data
Related structure data | 3b8sC 3b9dC 3b9eSC 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: 63843.855 Da / Num. of mol.: 1 / Fragment: Residues UNP 22-597 / Mutation: E315M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: LMG7890 / Description: Vibrio carchariae is synonym of Vibrio harveyi / Gene: chiA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AMP1, chitinase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% (w/v) PEG 4000, 0.1M magnesium chloride, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 53131 / Num. obs: 53131 / % possible obs: 99.7 % / Observed criterion σ(I): 26.3 / Redundancy: 8.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.074 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 6.1 / Num. unique all: 7564 / Rsym value: 0.332 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B9E Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.442 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 15.433 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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