+Open data
-Basic information
Entry | Database: PDB / ID: 7eap | ||||||
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Title | Crystal structure of IpeA-XXXG complex | ||||||
Components | Fn3_like domain-containing protein | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 3 / isoprimeverose-producing oligoxyloglucan hydrolase / xyloglucan oligosaccharides | ||||||
Function / homology | Function and homology information beta-glucosidase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K. | ||||||
Citation | Journal: Febs Lett. / Year: 2022 Title: Structural basis for the catalytic mechanism of the glycoside hydrolase family 3 isoprimeverose-producing oligoxyloglucan hydrolase from Aspergillus oryzae. Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eap.cif.gz | 338.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eap.ent.gz | 270.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/7eap ftp://data.pdbj.org/pub/pdb/validation_reports/ea/7eap | HTTPS FTP |
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-Related structure data
Related structure data | 5yotS S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 84029.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold) Strain: ATCC 42149 / RIB 40 / Gene: AO090701000274 / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q2U8V9 |
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-Sugars , 4 types, 9 molecules
#2: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 604 molecules
#5: Chemical | ChemComp-CA / |
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#7: 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: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 5.5, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 90 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: Oct 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→47.12 Å / Num. obs: 181988 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 0.995 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.42→1.47 Å / Num. unique obs: 17579 / CC1/2: 0.876 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YOT Resolution: 1.42→29.48 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.669 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / 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: 110.61 Å2 / Biso mean: 20.214 Å2 / Biso min: 11.13 Å2
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Refinement step | Cycle: final / Resolution: 1.42→29.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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