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Yorodumi- PDB-7c34: Crystal structure of Serratia marcescens Chitinase B complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c34 | ||||||
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Title | Crystal structure of Serratia marcescens Chitinase B complexed with Berberine | ||||||
Components | Chitinase | ||||||
Keywords | HYDROLASE / Serratia marcescens / Chitinase B / Berberine | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 Å | ||||||
Authors | Chen, L. / Chen, J. / Yang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2020 Title: Crystal structure-guided design of berberine-based novel chitinase inhibitors. Authors: Chen, L. / Zhu, L. / Chen, J. / Chen, W. / Qian, X. / Yang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c34.cif.gz | 384 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c34.ent.gz | 313.7 KB | Display | PDB format |
PDBx/mmJSON format | 7c34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/7c34 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/7c34 | HTTPS FTP |
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-Related structure data
Related structure data | 6jk9S 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: 55228.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Production host: Escherichia coli (E. coli) / References: UniProt: Q54276, UniProt: P11797*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.0 M ammonium sulfate, 10% glycerol, 100 mM HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97778 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.938→29.7807 Å / Num. obs: 81619 / % possible obs: 99.87 % / Redundancy: 7 % / Rsym value: 0.05 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.938→2.008 Å / Num. unique obs: 3868 / Rsym value: 0.235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6jk9 Resolution: 1.938→29.777 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.33 Å2 / Biso mean: 35.0354 Å2 / Biso min: 13.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.938→29.777 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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