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Yorodumi- PDB-4ate: High resolution crystal structure of beta-porphyranase A from Zob... -
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-Basic information
Entry | Database: PDB / ID: 4ate | ||||||
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Title | High resolution crystal structure of beta-porphyranase A from Zobellia galactanivorans | ||||||
Components | BETA-PORPHYRANASE A | ||||||
Keywords | HYDROLASE / AGAR DEGRADATION | ||||||
Function / homology | Function and homology information beta-porphyranase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / periplasmic space Similarity search - Function | ||||||
Biological species | ZOBELLIA GALACTANIVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å | ||||||
Authors | 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 | 4ate.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ate.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ate.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ate_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 4ate_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 4ate_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4ate_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4ate ftp://data.pdbj.org/pub/pdb/validation_reports/at/4ate | HTTPS FTP |
-Related 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: 30893.535 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) Description: ISOLATED FROM THE RED ALGAE DELESSERIA SANGUINEA AND DEPOSITED AT THE GERMAN COLLECTION OF MICROORGANISMS (DSM) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7GXG0, beta-porphyranase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.25 % Description: THE STRUCTURE WAS SOLVED BY MAD ON AN AURUM ION CONTAINING DERIVATIVE |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 18-20% PEG 4000, 0.2 M AMMONIUM SULFATE AND 0.1 M SODIUM ACETATE PH 4.6 AT 20 DEGREES C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→30.5 Å / Num. obs: 108086 / % possible obs: 99.9 % / Observed criterion σ(I): 0.01 / Redundancy: 10.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.1→25.86 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.606 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.897 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→25.86 Å
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Refine LS restraints |
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