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Yorodumi- PDB-4atf: Crystal structure of inactivated mutant beta-agarase B in complex... -
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-Basic information
Entry | Database: PDB / ID: 4atf | |||||||||
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Title | Crystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose | |||||||||
Components | BETA-AGARASE B | |||||||||
Keywords | HYDROLASE / POLYSACCHARIDASE / AGAROLYTIC ENZYME | |||||||||
Function / homology | Function and homology information beta-agarase / beta-agarase activity / cell outer membrane / carbohydrate metabolic process / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | ZOBELLIA GALACTANIVORANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Bernard, T. / Hehemann, J.H. / Correc, G. / Jam, M. / Michel, G. / Czjzek, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans. Authors: Hehemann, J.H. / Correc, G. / Thomas, F. / Bernard, T. / Barbeyron, T. / Jam, M. / Helbert, W. / Michel, G. / Czjzek, M. #1: Journal: Nature / Year: 2010 Title: Transfer of Carbohydrate-Active Enzymes from Marine Bacteria to Japanese Gut Microbiota. Authors: Hehemann, J. / Correc, G. / Barbeyron, T. / Helbert, W. / 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 | 4atf.cif.gz | 538 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4atf.ent.gz | 445.8 KB | Display | PDB format |
PDBx/mmJSON format | 4atf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4atf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4atf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4atf_validation.xml.gz | 60.2 KB | Display | |
Data in CIF | 4atf_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4atf ftp://data.pdbj.org/pub/pdb/validation_reports/at/4atf | HTTPS FTP |
-Related structure data
Related structure data | 4asmC 4ateC 1oyzS 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 68 - 340 / Label seq-ID: 22 - 294
NCS oper:
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-Components
#1: Protein | Mass: 35744.266 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 53-353 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) Description: IDENTIFIED AND ISOLATED FROM THE RED ALGAE DELESSERIA SANGUINEA AND FROM THE GERMAN COLLECTION OF MICROORGANISMS (DSM) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RGX8, beta-agarase #2: Polysaccharide | 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 189 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 189 TO ASP ...ENGINEERED | |
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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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 58% METHYL-PENTANE-DIOL, 20 MM CALCIUM CHLORIDE AND 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 6, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.4 Å / Num. obs: 357984 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OYZ Resolution: 1.9→65.35 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.248 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AGAROSE UNITS IN THE POSITIVE BINDING SITES WERE MODELED BUT NOT REFINED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→65.35 Å
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Refine LS restraints |
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