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Yorodumi- PDB-3b9e: Crystal structure of inactive mutant E315M chitinase A from Vibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9e | ||||||
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Title | Crystal structure of inactive mutant E315M chitinase A from Vibrio harveyi | ||||||
Components | Chitinase AChitinase A N-terminal domain | ||||||
Keywords | HYDROLASE / TIM-barrel / 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: 1.7 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 | 3b9e.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9e.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9e ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9e | HTTPS FTP |
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-Related structure data
Related structure data | 3b8sC 3b9aC 3b9dC 1ctnS S: Starting model for refinement C: citing same article (ref.) |
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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 / Mutation: E315M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: LMG7890 Description: VIBRIO HARVEYI was called formerly Vibrio carchariae Gene: CHIA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AMP1, chitinase |
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#2: 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: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEG 4000, 0.1M ammonium sulfate, 0.1M Tris-HCl pH 7.5, 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: Dec 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.68 Å / Num. all: 61563 / Num. obs: 61563 / % possible obs: 97.2 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.075 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.5 / Num. unique all: 7880 / Rsym value: 0.387 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CTN Resolution: 1.7→24.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.106 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / 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: 16.603 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→24.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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