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Yorodumi- PDB-7vc7: The structure of beta-xylosidase from Phanerochaete chrysosporium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vc7 | ||||||||||||
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Title | The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3) | ||||||||||||
Components | xylan 1,4-beta-xylosidase | ||||||||||||
Keywords | HYDROLASE / Glycoside hydrolase family 3 / beta-xylosidase / HYDROLASE (E.C.3.2.1.37) | ||||||||||||
Function / homology | DI(HYDROXYETHYL)ETHER / beta-D-xylopyranose Function and homology information | ||||||||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||||||||
Authors | Kojima, K. / Sunagawa, N. / Igarashi, K. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. Authors: Kojima, K. / Sunagawa, N. / Mikkelsen, N.E. / Hansson, H. / Karkehabadi, S. / Samejima, M. / Sandgren, M. / Igarashi, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vc7.cif.gz | 166.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vc7.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vc7_validation.pdf.gz | 805.7 KB | Display | wwPDB validaton report |
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Full document | 7vc7_full_validation.pdf.gz | 818.9 KB | Display | |
Data in XML | 7vc7_validation.xml.gz | 31 KB | Display | |
Data in CIF | 7vc7_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/7vc7 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/7vc7 | HTTPS FTP |
-Related structure data
Related structure data | 7vc6SC 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 , 1 types, 1 molecules A
#1: Protein | Mass: 79513.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: PcBxl3 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: xylan 1,4-beta-xylosidase |
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-Sugars , 2 types, 8 molecules
#5: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-XYP / | |
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-Non-polymers , 4 types, 186 molecules
#2: Chemical | ChemComp-1PE / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 525mM Malic acid (pH7.0), 20% v/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 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: Dec 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→44.08 Å / Num. obs: 14756 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 48.53 Å2 / CC1/2: 0.985 / Net I/σ(I): 7.82 |
Reflection shell | Resolution: 3.08→3.19 Å / Num. unique obs: 1450 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VC6 Resolution: 3.08→44.079 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→44.079 Å
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Refine LS restraints |
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LS refinement shell |
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