+Open data
-Basic information
Entry | Database: PDB / ID: 3wlh | |||||||||
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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 / plant apoplast | |||||||||
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: 1.65 Å | |||||||||
Authors | Streltsov, V.A. / Hrmova, M. | |||||||||
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 | 3wlh.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wlh.ent.gz | 229 KB | Display | PDB format |
PDBx/mmJSON format | 3wlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wlh ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wlh | HTTPS FTP |
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-Related structure data
Related structure data | 3wliC 3wljC 3wlkC 3wllC 3wlmC 3wlnC 3wloC 3wlpC 3wlqC 3wlrC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65475.617 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-630 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. vulgare (domesticated barley) Strain: Hordeum vulgare / References: UniProt: Q9XEI3 |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Non-polymers , 3 types, 842 molecules
#6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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-Details
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 |
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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: 3.57 Å3/Da / Density % sol: 65.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 75mM HEPES-NaOH pH7.0 buffer, 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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2007 Details: collimating mirror, double-crystal Si(111) monochromator |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→31.94 Å / Num. all: 106290 / Num. obs: 106290 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 13 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IEQ Resolution: 1.65→31.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.578 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.075 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→31.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.692 Å / Total num. of bins used: 20
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