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Yorodumi- PDB-7zei: Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zei | ||||||
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Title | Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A | ||||||
Components | Ch_Gaf159A | ||||||
Keywords | HYDROLASE / BETA PROPELLER / GALACTOFURANOSE / ARABINOFURANOSIDASE / CATALYSIS / EXO-HYDROLASE | ||||||
Function / homology | Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / Uncharacterized protein Function and homology information | ||||||
Biological species | Caldicellulosiruptor hydrothermalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Baudrexl, M. / Fida, T. / Berk, B. / Schwarz, W. / Zverlov, V.V. / Groll, M. / Liebl, W. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting alpha-L-Arabinofuranosidase Activity. Authors: Baudrexl, M. / Fida, T. / Berk, B. / Schwarz, W.H. / Zverlov, V.V. / Groll, M. / Liebl, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zei.cif.gz | 855.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zei.ent.gz | 706.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zei_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7zei_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7zei_validation.xml.gz | 85.2 KB | Display | |
Data in CIF | 7zei_validation.cif.gz | 126.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/7zei ftp://data.pdbj.org/pub/pdb/validation_reports/ze/7zei | HTTPS FTP |
-Related structure data
Related structure data | |
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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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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 37681.074 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor hydrothermalis (bacteria) Gene: Calhy_0274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4QB49 |
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-Non-polymers , 6 types, 2111 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-TRS / | #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: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES, 30% PEG 8000, 5% GLYCEROLE |
-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 EIGER2 S 16M / Detector: PIXEL / Date: Dec 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 269815 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 42069 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ALPHAFOLD2 Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.291 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.07 / 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: 89.5 Å2 / Biso mean: 22.72 Å2 / Biso min: 13.71 Å2
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Refinement step | Cycle: final / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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