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Yorodumi- PDB-5yqs: Isoprimeverose-producing enzyme from Aspergillus oryzae in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yqs | |||||||||
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Title | Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose | |||||||||
Components | Isoprimeverose-producing enzyme | |||||||||
Keywords | HYDROLASE / Glycoside hydrolase family 3 | |||||||||
Function / homology | Function and homology information beta-glucosidase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | Aspergillus oryzae RIB40 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Yaoi, K. / Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme. Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Fujimoto, Z. / Yaoi, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yqs.cif.gz | 316.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yqs.ent.gz | 257.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yqs ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yqs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 84087.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB 40 / Gene: AO090701000274 / Production host: Pichia (fungus) / Strain (production host): X-33 / References: UniProt: Q2U8V9 |
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-Sugars , 5 types, 22 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / #7: Sugar | ChemComp-BGC / | |
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-Non-polymers , 2 types, 554 molecules
#6: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH6.5, 26% PEG MME550, 0.15M CaCl2 |
-Data collection
Diffraction | Mean temperature: 173 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 14, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 59786 / % possible obs: 90.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Χ2: 3.533 / Net I/σ(I): 16.8 / Num. measured all: 178445 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.02 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 119.33 Å2 / Biso mean: 25.898 Å2 / Biso min: 6.1 Å2
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Refinement step | Cycle: final / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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