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Yorodumi- PDB-4ptm: Crystal Structure of Chitinase D from Serratia proteamaculans in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ptm | ||||||
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Title | Crystal Structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine, a hydrolyzed product of hexasaccharide at 1.7 Angstrom resolution | ||||||
Components | Glycoside hydrolase family 18 | ||||||
Keywords | HYDROLASE / Chitinase D / Chitinase / Glycoside hydrolase / Chtin / N-acetyl glucosamine | ||||||
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: 1.7 Å | ||||||
Authors | Kushwaha, G.S. / Madhuprakash, J. / Singh, A. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine, a hydrolyzed product of hexasaccharide at 1.7 Angstrom resolution Authors: Kushwaha, G.S. / Madhuprakash, J. / Singh, A. / Bhushan, A. / 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 | 4ptm.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ptm.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ptm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/4ptm ftp://data.pdbj.org/pub/pdb/validation_reports/pt/4ptm | 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
#1: Protein | Mass: 44514.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: 568 / Gene: Spro_2725 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GFD6, chitinase | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | #5: 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: 2.19 Å3/Da / Density % sol: 43.92 % |
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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2013 / Details: Mirrors |
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: 1.7→59.42 Å / Num. all: 43061 / Num. obs: 43061 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.034 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.89 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LGX Resolution: 1.7→59.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.295 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / 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: 18.977 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→59.42 Å
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