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Yorodumi- PDB-7o77: Structure of the PL6 family alginate lyase Patl3640 from Pseudoal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o77 | ||||||
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Title | Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c | ||||||
Components | Poly(Beta-D-mannuronate) lyase | ||||||
Keywords | LYASE / beta helix | ||||||
Function / homology | PL-6 family / Chondroitinase B / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Pectin lyase fold / Pectin lyase fold/virulence factor / Poly(Beta-D-mannuronate) lyase Function and homology information | ||||||
Biological species | Pseudoalteromonas atlantica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.321 Å | ||||||
Authors | Ballut, L. / Violot, S. / Carrique, L. / Aghajari, N. | ||||||
Citation | Journal: Glycobiology / Year: 2021 Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o77.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o77.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 7o77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/7o77 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o77 | HTTPS FTP |
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-Related structure data
Related structure data | 7o78C 7o79C 7o7aC 7o7tC 7o84C 5gkdS 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: 78834.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The two first residues (Met and Ala) are not visible in the electron density Source: (gene. exp.) Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087) (bacteria) Strain: T6c / ATCC BAA-1087 / Gene: Patl_3640 / Plasmid: pFO4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q15PP6, mannuronate-specific alginate lyase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Mg acetate, 0.1 M Na nitrate, 8% (w/v) PEG 10000, 0.15 mM CYMAL-7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.07 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→48.16 Å / Num. obs: 42777 / % possible obs: 97.3 % / Redundancy: 24.8 % / CC1/2: 1 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.32→2.46 Å / Num. unique obs: 5845 / CC1/2: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GKD Resolution: 2.321→48.16 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.239
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Displacement parameters | Biso max: 119.91 Å2 / Biso mean: 79.29 Å2 / Biso min: 43.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.321→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.321→2.35 Å / Rfactor Rfree error: 0
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