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Yorodumi- PDB-4q22: Crystal structure of Chitinase D from Serratia proteamaculans in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q22 | ||||||
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Title | Crystal structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine at 1.93 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: 1.93 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 at 1.93 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 | 4q22.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q22.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 4q22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q22 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q22 | 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 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GFD6, chitinase | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | ChemComp-ACT / | ||
#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: 43.9 % |
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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: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 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: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→59.22 Å / Num. all: 29280 / Num. obs: 29280 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.125 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.93→2 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 29280 / Rsym value: 0.301 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LGX Resolution: 1.93→59.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.523 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.138 / 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: 16.393 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→59.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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