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Yorodumi- PDB-5opq: A 3,6-anhydro-D-galactosidase produced by Zobellia galactanivoran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5opq | ||||||
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Title | A 3,6-anhydro-D-galactosidase produced by Zobellia galactanivorans. This is an exo-lytic enzyme that hydrolyzes terminal 3,6-anhydro-D-galactose from the non-reducing end of carrageenan oligosaccharides. | ||||||
Components | 3,6-anhydro-D-galactosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase 3 / 6-anhydro-D-galactosidase 3 / 6-anhydro-D-galactose carrageenan Zobellia galactanivorans | ||||||
Function / homology | Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Conserved hypothetical periplasmic protein Function and homology information | ||||||
Biological species | Zobellia galactanivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Ficko-Blean, E. / Michel, G. / Czjzek, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. ...Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. / Matard-Mann, M. / Stubbs, K.A. / Rogniaux, H. / Jeudy, A. / Barbeyron, T. / Medigue, C. / Czjzek, M. / Vallenet, D. / McBride, M.J. / Duchaud, E. / Michel, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5opq.cif.gz | 587.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5opq.ent.gz | 475.1 KB | Display | PDB format |
PDBx/mmJSON format | 5opq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5opq_validation.pdf.gz | 491.5 KB | Display | wwPDB validaton report |
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Full document | 5opq_full_validation.pdf.gz | 534.8 KB | Display | |
Data in XML | 5opq_validation.xml.gz | 123.2 KB | Display | |
Data in CIF | 5opq_validation.cif.gz | 185.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/5opq ftp://data.pdbj.org/pub/pdb/validation_reports/op/5opq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77935.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: zobellia_3152 / Production host: Escherichia coli (E. coli) / References: UniProt: G0L004 #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-TRS / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 1:1 ratio of 0.14M Na/K-tartrate, 12% PEG 3350 with 9 mg/ml ZGAL_3152 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→46.7 Å / Num. obs: 389746 / % possible obs: 99.6 % / Redundancy: 3.1 % / Net I/σ(I): 16.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→46.7 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.567 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.078 / 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: 21.082 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→46.7 Å
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Refine LS restraints |
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