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Yorodumi- PDB-4nzc: Crystal structure of Chitinase D from Serratia proteamaculans at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nzc | ||||||
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Title | Crystal structure of Chitinase D from Serratia proteamaculans at 1.45 Angstrom resolution | ||||||
Components | Glycoside hydrolase family 18 | ||||||
Keywords | HYDROLASE / Chitinase D / TIM barrel / Transglycosylation | ||||||
Function / homology | Function and homology information chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | Serratia proteamaculans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Madhuprakash, J. / Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P. | ||||||
Citation | Journal: Int J Biochem Mol Biol / Year: 2013 Title: Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation Authors: Madhuprakash, J. / Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nzc.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nzc.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzc ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzc | HTTPS FTP |
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-Related structure data
Related structure data | 4lgxS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44028.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: 568 / Gene: Spro_2725 / Plasmid: pET-22b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8GFD6, chitinase | ||
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#2: Chemical | ChemComp-ACT / | ||
#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: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 21, 2013 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→59.4 Å / Num. all: 69368 / Num. obs: 69368 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.099 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.316 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LGX Resolution: 1.45→59.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.152 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.075 / 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: 12.495 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→59.4 Å
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Refine LS restraints |
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