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Yorodumi- PDB-3n18: Crystal stricture of E145G/Y227F chitinase in complex with NAG fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n18 | |||||||||
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Title | Crystal stricture of E145G/Y227F chitinase in complex with NAG from Bacillus cereus NCTU2 | |||||||||
Components | Chitinase A | |||||||||
Keywords | HYDROLASE / Chitinase / ChiNCTU2 / complex / NAG / mutation | |||||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin binding / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus cereus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Hsieh, Y.-C. / Wu, Y.-J. / Wu, W.-G. / Li, Y.-K. / Chen, C.-J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structures of bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin-binding and insertion domains Authors: Hsieh, Y.-C. / Wu, Y.-J. / Chiang, T.-Y. / Kuo, C.-Y. / Shrestha, K.L. / Chao, C.-F. / Huang, Y.-C. / Chuankhayan, P. / Wu, W.-G. / Li, Y.-K. / Chen, C.-J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n18.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n18.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n18_validation.pdf.gz | 849.8 KB | Display | wwPDB validaton report |
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Full document | 3n18_full_validation.pdf.gz | 852.4 KB | Display | |
Data in XML | 3n18_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3n18_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/3n18 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n18 | HTTPS FTP |
-Related structure data
Related structure data | 3n11C 3n12SC 3n13C 3n15C 3n17C 3n1aC 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: 36179.562 Da / Num. of mol.: 1 / Mutation: E145G/Y227F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: NCTU2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / References: UniProt: D0VV09, 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 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Sequence details | THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. ACCORDING TO THE ...THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. ACCORDING TO THE ELECTRON DENSITY THE POSITION 277 IS OBVIOUSLY VAL THAN ALA. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20%(w/v) PEG 8000, 200mM calcium acetate in MES buffer(100mM, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 38407 / % possible obs: 98.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.031 / Rsym value: 0.045 / Net I/σ(I): 39.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3741 / Rsym value: 0.29 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N12 Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.813 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / 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: 18.411 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.642 Å / Total num. of bins used: 20
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