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Yorodumi- PDB-5fqh: The details of glycolipid glycan hydrolysis by the structural ana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fqh | |||||||||
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Title | The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens | |||||||||
Components | BETA-N-ACETYLGALACTOSAMINIDASE | |||||||||
Keywords | HYDROLASE / BETA-N-ACETYLGALACTOSAMINIDASE / GLYCOSIDE HYDROLASE / GH123 / GLYCOSPHINGOLIPID / GANGLIOSIDE / GLOBOSIDE / SUBSTRATE- ASSISTED CATALYSIS | |||||||||
Function / homology | Glycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / PHOSPHATE ION / Uncharacterized protein Function and homology information | |||||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Noach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium Perfringens Authors: Noach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fqh.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fqh.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fqh_validation.pdf.gz | 763.1 KB | Display | wwPDB validaton report |
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Full document | 5fqh_full_validation.pdf.gz | 765.2 KB | Display | |
Data in XML | 5fqh_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 5fqh_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fqh ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fqh | HTTPS FTP |
-Related structure data
Related structure data | 5fqeSC 5fqfC 5fqgC 5fr0C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 70232.266 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A0H2YNR7 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.43 Å3/Da / Density % sol: 49.49 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 |
Detector | Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.1 Å / Num. obs: 39970 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 11 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTR 5FQE Resolution: 2.1→96.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.024 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.185 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.214 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→96.24 Å
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Refine LS restraints |
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