+Open data
-Basic information
Entry | Database: PDB / ID: 3vlb | ||||||
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Title | Crystal structure of xeg-edgp | ||||||
Components |
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Keywords | PLANT PROTEIN/HYDROLASE / cell-wall / PLANT PROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / cellulase activity / polysaccharide catabolic process / cell wall organization / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Daucus carota (carrot) Aspergillus aculeatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Yoshizawa, T. / Shimizu, T. / Hirano, H. / Sato, M. / Hashimoto, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis for inhibition of xyloglucan-specific endo-beta-1,4-glucanase (XEG) by XEG-protein inhibitor Authors: Yoshizawa, T. / Shimizu, T. / Hirano, H. / Sato, M. / Hashimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vlb.cif.gz | 466.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vlb.ent.gz | 385.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vlb_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 3vlb_full_validation.pdf.gz | 489.7 KB | Display | |
Data in XML | 3vlb_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 3vlb_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/3vlb ftp://data.pdbj.org/pub/pdb/validation_reports/vl/3vlb | HTTPS FTP |
-Related structure data
Related structure data | 3vl8SC 3vl9C 3vlaSC 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: 43660.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Daucus carota (carrot) / Gene: EDGP1 / Cell (production host): carrot callus cell / Production host: Daucus carota (carrot) / References: UniProt: Q05929 #2: Protein | Mass: 23376.160 Da / Num. of mol.: 2 / Fragment: UNP residues 21-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: xgeA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O94218, xyloglucan-specific endo-beta-1,4-glucanase #3: 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: 2.91 Å3/Da / Density % sol: 57.72 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 40308 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VL8, 3VLA Resolution: 2.7→10 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.841 / SU B: 38.454 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R: 2.924 / ESU R Free: 0.478 / 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: 52.327 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / 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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