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Yorodumi- PDB-5ocq: Crystal structure of the complex of the kappa-carrageenase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ocq | ||||||
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Title | Crystal structure of the complex of the kappa-carrageenase from Pseudoalteromonas carrageenovora with an oligotetrasaccharide of kappa-carrageenan | ||||||
Components | Kappa-carrageenase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / kappa-carrageenase / beta jellyroll / marine carbohydrase | ||||||
Function / homology | Function and homology information kappa-carrageenase / kappa-carrageenase activity / periplasmic space / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Pseudoalteromonas carrageenovora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Czjzek, M. / Leroux, C. / Bernard, T. / Matard-Mann, M. / Jeudy, A. / Michel, G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural insights into marine carbohydrate degradation by family GH16 kappa-carrageenases. Authors: Matard-Mann, M. / Bernard, T. / Leroux, C. / Barbeyron, T. / Larocque, R. / Prechoux, A. / Jeudy, A. / Jam, M. / Nyvall Collen, P. / Michel, G. / Czjzek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ocq.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ocq.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 5ocq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/5ocq ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5ocq | HTTPS FTP |
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-Related structure data
Related structure data | 5ocrC 1dypS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32968.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas carrageenovora (bacteria) Gene: cgkA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P43478, kappa-carrageenase #2: Chemical | ChemComp-9RN / #3: Sugar | ChemComp-G4S / #4: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.0 M sodium citrate, 100 mM cacodylate pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→79 Å / Num. obs: 74710 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.966 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.071 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 25328 / Rsym value: 0.155 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DYP Resolution: 1.7→34.65 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.424 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.079 / 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: 13.086 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→34.65 Å
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Refine LS restraints |
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