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Yorodumi- PDB-5fui: Crystal structure of the C-terminal CBM6 of LamC a marine laminar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fui | |||||||||
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Title | Crystal structure of the C-terminal CBM6 of LamC a marine laminarianse from Zobellia galactanivorans | |||||||||
Components | ENDO-1,3-BETA-GLUCANASE, FAMILY GH16 | |||||||||
Keywords | HYDROLASE / CARBOHYDRATE BINDING MODULE / CBM6 / POLYSACCHARIDE FIXATION / MARINE BACTERIAL LAMINARINASE / ZOBELLIA GALACTANIVORANS | |||||||||
Function / homology | Function and homology information glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ZOBELLIA GALACTANIVORANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Labourel, A. / Jam, M. / Legentil, L. / Sylla, B. / Hehemann, J.H. / Ficko-Blean, E. / Ferrieres, V. / Czjzek, M. / Michel, G. | |||||||||
Citation | Journal: FEBS J. / Year: 2016 Title: Unraveling the Multivalent Binding of a Marine Family 6 Carbohydrate-Binding Module with its Native Laminarin Ligand. Authors: Jam, M. / Ficko-Blean, E. / Labourel, A. / Larocque, R. / Czjzek, M. / Michel, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fui.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fui.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fui_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 5fui_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5fui_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 5fui_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fui ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fui | HTTPS FTP |
-Related structure data
Related structure data | 1uxzS S: Starting model for refinement |
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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: 14512.704 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 262-385 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: GOL2L9, UniProt: G0L2L9*PLUS | ||||||
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#2: Chemical | ChemComp-GOL / | ||||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | THE CRYSTAL STRUCTURE CONTAINS THE CENTRAL CBM6 MODULE ONLY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % / Description: NONE |
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Crystal grow | pH: 7.2 Details: 100 MM HEPES PH 7.2, 10 MM MGCL2 AND 27 % POLYACRYLIC ACID. MICROSEEDING WAS ESSENTIAL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.7 Å / Num. obs: 19499 / % possible obs: 93 % / Observed criterion σ(I): 0.1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 65.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UXZ Resolution: 1.4→46.71 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.346 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→46.71 Å
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Refine LS restraints |
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