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Yorodumi- PDB-4be3: crystal structure of the exolytic PL7 alginate lyase AlyA5 from Z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4be3 | ||||||
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Title | crystal structure of the exolytic PL7 alginate lyase AlyA5 from Zobellia galactanivorans | ||||||
Components | ALGINATE LYASE, FAMILY PL7 | ||||||
Keywords | LYASE / FLAVOBACTERIUM | ||||||
Function / homology | Function and homology information mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity Similarity search - Function | ||||||
Biological species | ZOBELLIA GALACTANIVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Thomas, F. / Jeudy, A. / Michel, G. / Czjzek, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Comparative Characterization of Two Marine Alginate Lyases from Zobellia Galactanivorans Reveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate. Authors: Thomas, F. / Lundqvist, L.C.E. / Jam, M. / Jeudy, A. / Barbeyron, T. / Sandstrom, C. / 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 | 4be3.cif.gz | 273 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4be3.ent.gz | 220.4 KB | Display | PDB format |
PDBx/mmJSON format | 4be3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4be3_validation.pdf.gz | 484.2 KB | Display | wwPDB validaton report |
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Full document | 4be3_full_validation.pdf.gz | 507.8 KB | Display | |
Data in XML | 4be3_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 4be3_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4be3 ftp://data.pdbj.org/pub/pdb/validation_reports/be/4be3 | HTTPS FTP |
-Related structure data
Related structure data | 3zpyC 2z42S C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35275.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) Description: ROSCOFF INHOUSE CULTURE AND ISOLATE AND GERMAN COLLECTION OF MICROORGANISMS (DSM) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: G0L2Y1, guluronate-specific alginate lyase, mannuronate-specific alginate lyase |
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-Non-polymers , 5 types, 583 molecules
#2: Chemical | ChemComp-SRT / |
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#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-TAR / |
#5: Chemical | ChemComp-TLA / |
#6: 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: 3.63 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | pH: 7 Details: 22% PEG 3350 AND 0.2 M SODIUM/POTASSIUM TARTRATE, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→41.95 Å / Num. obs: 114168 / % possible obs: 99.4 % / Observed criterion σ(I): 0.1 / Redundancy: 8.47 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.53 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.3 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z42 Resolution: 1.75→41.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.985 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED USING LOWERED OCCUPATION FACTORS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED USING LOWERED OCCUPATION FACTORS FOR SIDE CHAINS OF NOT WELL DEFINED RESIDUES
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.959 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→41.95 Å
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Refine LS restraints |
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