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Yorodumi- PDB-6jg1: Crystal structure of barley exohydrolaseI wildtype in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jg1 | ||||||
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Title | Crystal structure of barley exohydrolaseI wildtype in complex with 4I,4III,4V-S-trithiocellohexaose | ||||||
Components | Barley exohydrolase I | ||||||
Keywords | HYDROLASE / Barley exohydrolaseI / enzyme function | ||||||
Function / homology | Function and homology information beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Hordeum vulgare subsp. vulgare (domesticated barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Luang, S. / Streltsov, V.A. / Hrmova, M. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Authors: Luang, S. / Fernandez-Luengo, X. / Nin-Hill, A. / Streltsov, V.A. / Schwerdt, J.G. / Alonso-Gil, S. / Ketudat Cairns, J.R. / Pradeau, S. / Fort, S. / Marechal, J.D. / Masgrau, L. / Rovira, C. / Hrmova, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jg1.cif.gz | 257.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jg1.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/6jg1 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/6jg1 | HTTPS FTP |
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-Related structure data
Related structure data | 6jg2C 6jg6C 6jg7C 6jgaC 6jgbC 6jgcC 6jgdC 6jgeC 6jggC 6jgkC 6jglC 6jgnC 6jgoC 6jgpC 6jgqC 6jgrC 6jgsC 6jgtC 6k6vC 6kufC 6l1jC 6lbbC 6lbvC 6lc5C 3wliS 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: 65894.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley) Plasmid: PPICZALPHABNH8/DEST / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A287SCR5, UniProt: Q9XEI3*PLUS |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose / thio-beta-cellobiose |
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#3: Sugar |
-Non-polymers , 4 types, 559 molecules
#4: Chemical | ChemComp-1PE / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | Amino acid at the position 320 should be Lysine. However, the electron density map is not clear, ...Amino acid at the position 320 should be Lysine. However, the electron density map is not clear, probably side chain of this residue is flexible |
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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: 3.46 Å3/Da / Density % sol: 64.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2012 / Details: COLLIMATING MIRROR |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.17 Å / Num. obs: 84211 / % possible obs: 99.91 % / Redundancy: 29 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.78→1.83 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 121651 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WLI Resolution: 1.78→48.17 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.652 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.743 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→48.17 Å
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Refine LS restraints |
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