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Yorodumi- PDB-4lgx: Structure of Chitinase D from Serratia proteamaculans revealed an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lgx | ||||||
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Title | Structure of Chitinase D from Serratia proteamaculans revealed an unusually constrained substrate binding site | ||||||
Components | Glycoside hydrolase family 18 | ||||||
Keywords | HYDROLASE / TIM BARREL | ||||||
Function / homology | Function and homology information chitinase / 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: 1.49 Å | ||||||
Authors | Madhuprakash, J. / Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Inverse relationship between chitobiase and transglycosylation activities of chitinase-D from Serratia proteamaculans revealed by mutational and biophysical analyses. Authors: Madhuprakash, J. / Bobbili, K.B. / Moerschbacher, B.M. / Singh, T.P. / Swamy, M.J. / Podile, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lgx.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lgx.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lgx ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lgx | HTTPS FTP |
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-Related structure data
Related structure data | 3qokS 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: 44773.375 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: 2.18 Å3/Da / Density % sol: 43.67 % |
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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: Apr 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: 1.49→35.19 Å / Num. all: 64748 / Num. obs: 64748 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.05 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 1.49→1.52 Å / Mean I/σ(I) obs: 6.1 / Rsym value: 0.25 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QOK Resolution: 1.49→35.19 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.066 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.436 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→35.19 Å
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Refine LS restraints |
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