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Yorodumi- PDB-6m55: Crystal structure of the E496A mutant of HsBglA in complex with 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m55 | |||||||||
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Title | Crystal structure of the E496A mutant of HsBglA in complex with 4-galactosyllactose | |||||||||
Components | Beta-galactosidase-like enzyme | |||||||||
Keywords | HYDROLASE / galactooligosaccharide / transgalactosylation / beta-galactosidase / beta-glucosidase / Hamamotoa singularis / STRUCTURAL PROTEIN | |||||||||
Function / homology | Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / beta-glucosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / metal ion binding / alpha-D-mannopyranose / Beta-galactosidase-like enzyme Function and homology information | |||||||||
Biological species | Hamamotoa singularis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Uehara, R. / Iwamoto, R. / Aoki, S. / Yoshizawa, T. / Takano, K. / Matsumura, H. / Tanaka, S.-i. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Crystal structure of a GH1 beta-glucosidase from Hamamotoa singularis. Authors: Uehara, R. / Iwamoto, R. / Aoki, S. / Yoshizawa, T. / Takano, K. / Matsumura, H. / Tanaka, S.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m55.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m55.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m55_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6m55_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6m55_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 6m55_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m55 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m55 | HTTPS FTP |
-Related structure data
Related structure data | 6m4eC 6m4fC 4gxpS 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 / Non-polymers , 2 types, 5 molecules AD
#1: Protein | Mass: 60452.949 Da / Num. of mol.: 2 / Mutation: E496A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hamamotoa singularis (fungus) / Gene: bglA / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q564N5 #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 10 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | ChemComp-NAG / |
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-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: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M SPG Buffer pH 7.0, 27% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→45.99 Å / Num. obs: 24658 / % possible obs: 96.66 % / Redundancy: 6.1 % / Biso Wilson estimate: 57.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1612 / Rpim(I) all: 0.06944 / Rrim(I) all: 0.1759 / Net I/σ(I): 7.27 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5642 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 1795 / CC1/2: 0.912 / Rpim(I) all: 0.2658 / Rrim(I) all: 0.6255 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GXP Resolution: 3→45.21 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.8 Å2 / Biso mean: 55.3936 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→45.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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