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Yorodumi- PDB-7f7q: Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f7q | ||||||
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Title | Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455A in complex with p-nitrophenyl alpha-N-acetylgalactosaminide | ||||||
Components | GH31 alpha-N-acetylgalactosaminidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH31 / mucin / (BETA/ALPHA)8-BARREL / FIBRONECTIN-LIKE / substrate / complex | ||||||
Function / homology | 2-acetamido-2-deoxy-alpha-D-galactopyranose / P-NITROPHENOL Function and homology information | ||||||
Biological species | Enterococcus faecalis ATCC 10100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Miyazaki, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochimie / Year: 2022 Title: Structural and mechanistic insights into the substrate specificity and hydrolysis of GH31 alpha-N-acetylgalactosaminidase. Authors: Miyazaki, T. / Ikegaya, M. / Alonso-Gil, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7q.cif.gz | 343.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7q.ent.gz | 262.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f7q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7f7q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7f7q_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 7f7q_validation.cif.gz | 62.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7q ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7q | HTTPS FTP |
-Related structure data
Related structure data | 7f7rC 6m76S 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, 2 molecules A
#1: Protein | Mass: 106584.633 Da / Num. of mol.: 1 / Mutation: D455A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis ATCC 10100 (bacteria) Gene: WOW_01747 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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#2: Sugar | ChemComp-A2G / |
-Non-polymers , 4 types, 802 molecules
#3: Chemical | ChemComp-NPO / | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2 M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. obs: 184729 / % possible obs: 98 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.42→1.5 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 25867 / CC1/2: 0.766 / Rpim(I) all: 0.29 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M76 Resolution: 1.42→42.139 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.192 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.061 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: 22.221 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→42.139 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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