+Open data
-Basic information
Entry | Database: PDB / ID: 3wlr | ||||||
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Title | Crystal Structure Analysis of Plant Exohydrolase | ||||||
Components | Beta-D-glucan exohydrolase isoenzyme ExoI | ||||||
Keywords | HYDROLASE / BETA BARREL / GRAIN DEVELOPMENT / Enzyme Function Initiative / Tim Barrel/Beta sheet / N-glycosylation | ||||||
Function / homology | Function and homology information beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Hordeum vulgare subsp. vulgare (domesticated barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Streltsov, V.A. / Hrmova, M. / Luang, S. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / ...Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / Mendoza, F. / Tiessler-Sala, L. / Sanchez-Aparicio, J.E. / Rodriguez-Guerra, J. / Lluch, J.M. / Marechal, J.D. / Masgrau, L. / Hrmova, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wlr.cif.gz | 145 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wlr.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wlr ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wlr | HTTPS FTP |
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-Related structure data
Related structure data | 3wlhC 3wliC 3wljC 3wlkC 3wllC 3wlmC 3wlnC 3wloC 3wlpC 3wlqC 6md6C 6mi1C 1ieqS 3wlt 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
#1: Protein | Mass: 65749.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-630 / Mutation: R158A, E161A 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) / Strain (production host): SMD11680H References: UniProt: Q9XEI3, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||||
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#2: Sugar | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING OF AF102868 (GENBANK ACCESSION NUMBER). ...THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 75mM HEPES-NaOH pH7.0, 1.2% PEG 400, 1.7M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9615 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / 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: 0.9615 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→46.37 Å / Num. all: 45206 / Num. obs: 45206 / % possible obs: 98.8 % |
Reflection shell | Resolution: 2.21→2.26 Å / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.4 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEQ Resolution: 2.21→46.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.903 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→46.37 Å
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Refine LS restraints |
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