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Yorodumi- PDB-7xtj: Crystal structure of E88A mutant of GH3 beta-xylosidase from Aspe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xtj | ||||||
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Title | Crystal structure of E88A mutant of GH3 beta-xylosidase from Aspergillus niger (AnBX) | ||||||
Components | Xylan 1,4-beta-xylosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH3 | ||||||
Function / homology | Function and homology information xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kaenying, W. / Kongsaeree, P.T. / Tagami, T. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2023 Title: Crystal structure and identification of amino acid residues for catalysis and binding of GH3 AnBX beta-xylosidase from Aspergillus niger. Authors: Kaenying, W. / Choengpanya, K. / Tagami, T. / Wattana-Amorn, P. / Lang, W. / Okuyama, M. / Li, Y.K. / Kimura, A. / Kongsaeree, P.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xtj.cif.gz | 368 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xtj.ent.gz | 240.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xtj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7xtj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7xtj_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 7xtj_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtj ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtj | HTTPS FTP |
-Related structure data
Related structure data | 6q7iS S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 85819.586 Da / Num. of mol.: 2 / Mutation: E88A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Strain: ASKU28 / Plasmid: Opt-pPICZaBNH8 / Production host: Komagataella pastoris (fungus) / Strain (production host): Y11430 / References: UniProt: A0A023J5W7, xylan 1,4-beta-xylosidase |
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-Sugars , 4 types, 13 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 35 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 16% (v/v) ethylene glycol, 0.1 M citric acid, pH 3.5, 10% (w/v) polyethylene glycol 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 68702 / % possible obs: 99.8 % / Redundancy: 27.1 % / Biso Wilson estimate: 59.53 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.244 / Rsym value: 0.24 / Net I/σ(I): 14.49 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 27 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 10817 / CC1/2: 0.684 / Rrim(I) all: 3.31 / Rsym value: 3.26 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q7I Resolution: 2.5→49.97 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9953 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.97 Å
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Refine LS restraints |
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LS refinement shell |
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