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Yorodumi- PDB-8j50: Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j50 | ||||||
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Title | Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase | ||||||
Components | GH31 alpha-galactosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / (beta/alpha)8 barrel / Globo sphingolipid / glycolipid / Carbohydrate | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Flavihumibacter petaseus NBRC 106054 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ikegaya, M. / Miyazaki, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose. Authors: Ikegaya, M. / Park, E.Y. / Miyazaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j50.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8j50.ent.gz | 671.7 KB | Display | PDB format |
PDBx/mmJSON format | 8j50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/8j50 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j50 | HTTPS FTP |
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-Related structure data
Related structure data | 8j51C 8j52C 8j53C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60973.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavihumibacter petaseus NBRC 106054 (bacteria) Strain: NBRC 106054 / Gene: FPE01S_01_01430 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E9MUN5, alpha-galactosidase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.11 Å3/Da / Density % sol: 60.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M sodium chloride, 50 mM MES-NaOH |
-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: May 15, 2022 |
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→46.09 Å / Num. obs: 111441 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.079 / Rrim(I) all: 0.112 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4433 / CC1/2: 0.77 / Rpim(I) all: 0.437 / Rrim(I) all: 0.618 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.415 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.13 / SU B: 6.331 / SU ML: 0.078 / Average fsc free: 0.9761 / Average fsc work: 0.9861 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.102 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: 27.542 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.415 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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