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Yorodumi- PDB-5olc: Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5olc | |||||||||
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Title | Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from Zobellia galactanivorans | |||||||||
Components | Galactonate dehydratase | |||||||||
Keywords | ISOMERASE / cycloisomerase / enolase superfamily / 3 / 6-anhydro-D-galactonate / carrageenan | |||||||||
Function / homology | Function and homology information galactonate dehydratase / galactonate dehydratase activity / amino acid catabolic process Similarity search - Function | |||||||||
Biological species | Zobellia galactanivorans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | |||||||||
Authors | Michel, G. / Czjzek, M. / Jam, M. | |||||||||
Funding support | France, 2items
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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 | 5olc.cif.gz | 539.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5olc.ent.gz | 441.6 KB | Display | PDB format |
PDBx/mmJSON format | 5olc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5olc_validation.pdf.gz | 515.9 KB | Display | wwPDB validaton report |
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Full document | 5olc_full_validation.pdf.gz | 563.8 KB | Display | |
Data in XML | 5olc_validation.xml.gz | 92.4 KB | Display | |
Data in CIF | 5olc_validation.cif.gz | 125.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/5olc ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5olc | HTTPS FTP |
-Related structure data
Related structure data | 5opqC 4hpnS 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: 44897.438 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: dgoD, zobellia_3156 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L7B8, galactonate dehydratase #2: Chemical | ChemComp-MG / #3: 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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: Optimized conditions were a 1:1 ratio of 0.2 M tri potassium citrate, 20% PEG 3350 to 25 mg/ml ZGAL_3156. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→49.17 Å / Num. obs: 93118 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 79.39 Å2 / CC1/2: 0.978 / Net I/σ(I): 3.97 |
Reflection shell | Resolution: 2.79→2.87 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.87 / CC1/2: 0.473 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HPN Resolution: 2.79→49.17 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.913 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.361
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Displacement parameters | Biso mean: 68.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.79→49.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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