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Yorodumi- PDB-3ur8: Lower-density crystal structure of potato endo-1,3-beta-glucanase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ur8 | ||||||
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Title | Lower-density crystal structure of potato endo-1,3-beta-glucanase | ||||||
Components | Glucan endo-1,3-beta-D-glucosidase | ||||||
Keywords | HYDROLASE / glucoside hydrolase / GH17 family / pathogenesis-related class-2 protein (PR-2) / TIM Barrel / Glycoside Hydrolase / Carbohydrate/Sugar Binding | ||||||
Function / homology | Function and homology information glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / defense response / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Wojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Two high-resolution structures of potato endo-1,3-beta-glucanase reveal subdomain flexibility with implications for substrate binding Authors: Wojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M. #1: Journal: Acta Biochim.Pol. / Year: 2008 Title: Conserved Cys residue influences catalytic properties of potato endo-(1-->3)-beta-glucanase GLUB20-2. Authors: Witek, A.I. / Witek, K. / Hennig, J. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities. Authors: Varghese, J.N. / Garrett, T.P. / Colman, P.M. / Chen, L. / Hoj, P.B. / Fincher, G.B. #3: Journal: Proteins / Year: 2006 Title: Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome. Authors: Receveur-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J. / Rouge, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ur8.cif.gz | 290.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ur8.ent.gz | 233.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ur8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ur8_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 3ur8_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 3ur8_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 3ur8_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/3ur8 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3ur8 | HTTPS FTP |
-Related structure data
Related structure data | 3ur7SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36608.969 Da / Num. of mol.: 2 Fragment: mature endo-1,3-beta-glucanase, UNP residues 24-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Strain: Desiree / Gene: gluB20-2 / Plasmid: pET-30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q70C53, glucan endo-1,3-beta-D-glucosidase #2: Water | ChemComp-HOH / | |
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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: 2.03 Å3/Da / Density % sol: 39.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Feb 4, 2007 / Details: mirrors |
Radiation | Monochromator: Ge(111) triangular bent crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8148 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→40 Å / Num. all: 151662 / Num. obs: 151662 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.26→1.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2 / Num. unique all: 14787 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UR7 Resolution: 1.26→19.54 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.485 / SU ML: 0.029 Isotropic thermal model: Anisotropic model of ADP parameters Cross valid method: R free / ESU R Free: 0.046 / Stereochemistry target values: Engh & Huber Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. ANISOTROPIC ADP REFINEMENT.
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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 mean: 9.348 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.29 Å / Total num. of bins used: 20
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