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Yorodumi- PDB-4u6b: Zg3597, a family 117 glycoside hydrolase, produced by the marine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u6b | ||||||
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Title | Zg3597, a family 117 glycoside hydrolase, produced by the marine bacterium Zobellia galactanivorans | ||||||
Components | Conserved hypothetical lipoprotein | ||||||
Keywords | HYDROLASE / GH117 | ||||||
Function / homology | Function and homology information metabolic process / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | Zobellia galactanivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ficko-Blean, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic ...Title: Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family. Authors: Ficko-Blean, E. / Duffieux, D. / Rebuffet, E. / Larocque, R. / Groisillier, A. / 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 | 4u6b.cif.gz | 303.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u6b.ent.gz | 242.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u6b_validation.pdf.gz | 508 KB | Display | wwPDB validaton report |
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Full document | 4u6b_full_validation.pdf.gz | 541.1 KB | Display | |
Data in XML | 4u6b_validation.xml.gz | 61 KB | Display | |
Data in CIF | 4u6b_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/4u6b ftp://data.pdbj.org/pub/pdb/validation_reports/u6/4u6b | HTTPS FTP |
-Related structure data
Related structure data | 4u6dC 3p2nS 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48758.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij / Gene: zobellia_3597 / Production host: Escherichia coli (E. coli) References: UniProt: F0V1E1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Non-polymers , 6 types, 723 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-ACY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: The optimized crystallization conditions for Zg3597 were: 16% glycerol, 0.15 M ammonium sulfate, and 20 % PEG 4000 in a 1:1 ratio with protein at 5 and 2.5 mg/mL and 14% PEG 3350 and 75 mM ...Details: The optimized crystallization conditions for Zg3597 were: 16% glycerol, 0.15 M ammonium sulfate, and 20 % PEG 4000 in a 1:1 ratio with protein at 5 and 2.5 mg/mL and 14% PEG 3350 and 75 mM sodium acetate with a ratio of 2:1 protein (at 7.5 mg/mL) to mother liquor. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 103865 / % possible obs: 99.7 % / Redundancy: 6 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.3→2.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P2N Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.786 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 38.537 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→30 Å
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Refine LS restraints |
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