+Open data
-Basic information
Entry | Database: PDB / ID: 7uql | ||||||
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Title | Pathogenesis related 10-10 app from | ||||||
Components | Pathogenesis Related 10-10 protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / binding protein / alkaloids / opium poppy | ||||||
Biological species | Papaver somniferum (opium poppy) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Carr, S.C. / Ng, K.K.S. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation. Authors: Ozber, N. / Carr, S.C. / Morris, J.S. / Liang, S. / Watkins, J.L. / Caldo, K.M. / Hagel, J.M. / Ng, K.K.S. / Facchini, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uql.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uql.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 7uql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uql_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 7uql_full_validation.pdf.gz | 435.7 KB | Display | |
Data in XML | 7uql_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7uql_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/7uql ftp://data.pdbj.org/pub/pdb/validation_reports/uq/7uql | HTTPS FTP |
-Related structure data
Related structure data | 7uqmC 7uqnC 7uqoC 6ka3S S: Starting model for refinement C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17625.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Papaver somniferum (opium poppy) / Production host: Escherichia coli (E. coli) #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: 2.41 Å3/Da / Density % sol: 49.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.6 Å / Num. obs: 27479 / % possible obs: 98.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 34.66 Å2 / CC1/2: 1 / Net I/σ(I): 27.42 |
Reflection shell | Resolution: 1.9→1.95 Å / Num. unique obs: 1977 / CC1/2: 0.849 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KA3 Resolution: 1.9→35.09 Å / SU ML: 0.2218 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1148 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.09 Å
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Refine LS restraints |
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LS refinement shell |
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