+Open data
-Basic information
Entry | Database: PDB / ID: 6gl2 | ||||||
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Title | Structure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution | ||||||
Components | Endoglucanase, family GH5Cellulase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH5 / Mixed linked glucan / Zobellia galactanivorans | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Zobellia galactanivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Dorival, J. / Ruppert, S. / Gunnoo, M. / Orlowski, A. / Chapelais, M. / Dabin, J. / Labourel, A. / Thompson, D. / Michel, G. / Czjzek, M. / Genicot, S. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: The laterally acquired GH5ZgEngAGH5_4from the marine bacteriumZobellia galactanivoransis dedicated to hemicellulose hydrolysis. Authors: Dorival, J. / Ruppert, S. / Gunnoo, M. / Orlowski, A. / Chapelais-Baron, M. / Dabin, J. / Labourel, A. / Thompson, D. / Michel, G. / Czjzek, M. / Genicot, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gl2.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gl2.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/6gl2 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/6gl2 | HTTPS FTP |
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-Related structure data
Related structure data | 6gl0C 3ndzS S: Starting model for refinement C: citing same article (ref.) |
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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: 38438.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: engA, zobellia_208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L8Z3, cellulase | ||
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#2: Chemical | #3: 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: 2.01 Å3/Da / Density % sol: 38.75 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 14% PEG 6000, 200 mM CaCl2, 100 mM M sodium acetate buffer at pH 5.0 PH range: none |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→57.41 Å / Num. obs: 99084 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.16 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.18→1.24 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 14405 / CC1/2: 0.43 / Rrim(I) all: 0.74 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NDZ Resolution: 1.96→57.41 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.741 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.045 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.635 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→57.41 Å
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Refine LS restraints |
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