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Yorodumi- PDB-6l1j: Crystal structure of barley exohydrolaseI W434A mutant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l1j | ||||||
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Title | Crystal structure of barley exohydrolaseI W434A mutant in complex with 4'-nitrophenyl thiolaminaritrioside | ||||||
Components | BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 | ||||||
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: 1.8 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 | 6l1j.cif.gz | 258.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l1j.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 6l1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/6l1j ftp://data.pdbj.org/pub/pdb/validation_reports/l1/6l1j | HTTPS FTP |
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-Related structure data
Related structure data | 6jg1C 6jg2C 6jg6C 6jg7C 6jgaC 6jgbC 6jgcC 6jgdC 6jgeC 6jggC 6jgkC 6jglC 6jgnC 6jgoC 6jgpC 6jgqC 6jgrC 6jgsC 6jgtC 6k6vC 6kufC 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 / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 65778.938 Da / Num. of mol.: 1 / Mutation: W434A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley) Production host: Komagataella pastoris (fungus) / References: UniProt: A0A287SCR5, UniProt: Q9XEI3*PLUS |
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#2: Sugar |
-Non-polymers , 6 types, 702 molecules
#3: Chemical | ChemComp-LAM / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-1PE / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.07 % |
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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: 1.8→88.23 Å / Num. obs: 83048 / % possible obs: 99.8 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 51.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.055 / Num. unique obs: 6011 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WLI Resolution: 1.8→27.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.846 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.48 Å2 / Biso mean: 23.809 Å2 / Biso min: 12.56 Å2
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Refinement step | Cycle: final / Resolution: 1.8→27.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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