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Yorodumi- PDB-6m77: GH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m77 | ||||||
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Title | GH31 alpha-N-acetylgalactosaminidase from Enterococcus faecalis in complex with N-acetylgalactosamine | ||||||
Components | LPXTG-motif cell wall anchor domain protein | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / MUCIN / (BETA/ALPHA)8-BARREL / FIBRONECTIN-LIKE | ||||||
Function / homology | Domain of unknown function (DUF5110) / Glycosyl hydrolases family 31 TIM-barrel domain / 2-acetamido-2-deoxy-beta-D-galactopyranose Function and homology information | ||||||
Biological species | Enterococcus faecalis ATCC 10100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Miyazaki, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs Lett. / Year: 2020 Title: Crystal structure of the Enterococcus faecalis alpha-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31. Authors: Miyazaki, T. / Park, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m77.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m77.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 6m77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m77_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6m77_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6m77_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 6m77_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/6m77 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/6m77 | HTTPS FTP |
-Related structure data
Related structure data | 6m76SC 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
#1: Protein | Mass: 106628.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis ATCC 10100 (bacteria) Strain: ATCC 10100 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) | ||||||||
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#2: Sugar | ChemComp-NGA / | ||||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG3350, 0.2 M ammonium citrate, 5 mM N-acetylgalactosamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 80809 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 11575 / CC1/2: 0.844 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M76 Resolution: 1.9→40.091 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.21 / SU B: 4.774 / SU ML: 0.134 / Average fsc free: 0.8527 / Average fsc work: 0.8767 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.157 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.848 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.091 Å
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Refine LS restraints |
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LS refinement shell |
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