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- PDB-5fqf: The details of glycolipid glycan hydrolysis by the structural ana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fqf | ||||||
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Title | The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens | ||||||
![]() | BETA-N-ACETYLGALACTOSAMINIDASE | ||||||
![]() | 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 / FORMIC ACID / 2-acetamido-2-deoxy-beta-D-galactopyranose / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 214.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 50.1 KB | Display | |
Data in CIF | ![]() | 74.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fqeSC ![]() 5fqgC ![]() 5fqhC ![]() 5fr0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 70234.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-NGA / #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.89 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→70 Å / Num. obs: 72256 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FQE Resolution: 2.15→87.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.718 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.169 / 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: 21.851 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→87.37 Å
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Refine LS restraints |
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