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Yorodumi- PDB-6hm1: Structural and thermodynamic signatures of ligand binding to an e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hm1 | ||||||||||||
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Title | Structural and thermodynamic signatures of ligand binding to an enigmatic chitinase-D from Serratia proteamaculans | ||||||||||||
Components | Glycoside hydrolase family 18 | ||||||||||||
Keywords | HYDROLASE / Chitinase / CARBOHYDRATE | ||||||||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | Serratia proteamaculans (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||||||||
Authors | Madhuprakash, J. / Dalhus, B. / Vaaje-Kolstad, G. / Eijsink, V.G.H. / Sorlie, M. | ||||||||||||
Funding support | Norway, India, 3items
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Citation | Journal: J.Phys.Chem.B / Year: 2019 Title: Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans. Authors: Madhuprakash, J. / Dalhus, B. / Vaaje-Kolstad, G. / Sakuda, S. / Podile, A.R. / Eijsink, V.G.H. / Sorlie, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hm1.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hm1.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hm1_validation.pdf.gz | 791.1 KB | Display | wwPDB validaton report |
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Full document | 6hm1_full_validation.pdf.gz | 791.5 KB | Display | |
Data in XML | 6hm1_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6hm1_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hm1 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hm1 | HTTPS FTP |
-Related structure data
Related structure data | 4nzcS 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: 44201.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria) Strain: 568 / Gene: Spro_2725 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: A8GFD6 | ||
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#2: Chemical | ChemComp-AO3 / | ||
#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: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5 and 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97319 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97319 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→43.69 Å / Num. obs: 57471 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5508 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4nzc Resolution: 1.54→43.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→43.69 Å
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Refine LS restraints |
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LS refinement shell |
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