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Yorodumi- PDB-4u6d: Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u6d | ||||||
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Title | Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6-anhydro-L-galactose | ||||||
Components | Conserved hypothetical periplasmic protein | ||||||
Keywords | HYDROLASE / GH117 / bicyclic sugar | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Zobellia galactanivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 4u6d.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u6d.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u6d_validation.pdf.gz | 496.7 KB | Display | wwPDB validaton report |
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Full document | 4u6d_full_validation.pdf.gz | 508.9 KB | Display | |
Data in XML | 4u6d_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 4u6d_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/4u6d ftp://data.pdbj.org/pub/pdb/validation_reports/u6/4u6d | HTTPS FTP |
-Related structure data
Related structure data | 4u6bSC 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 / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 47501.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Strain: DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij / Gene: zobellia_3615 / Production host: Escherichia coli (E. coli) References: UniProt: F0V1E2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #5: Sugar | ChemComp-3DY / | |
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-Non-polymers , 4 types, 735 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: The optimized condition for Zg3615 was: 0.1 M sodium acetate pH 5.0, 25% PEG 3350, in a 1:1 ratio of protein (at 10 mg/mL) to mother liquor. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 96642 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U6B Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.947 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.37 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→30 Å
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Refine LS restraints |
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