+Open data
-Basic information
Entry | Database: PDB / ID: 6uop | ||||||||||||
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Title | OsPYL/RCAR5 (24 - 29) solved by nanobeam diffraction tomography | ||||||||||||
Components | Abscisic acid receptor PYL5 | ||||||||||||
Keywords | PROTEIN FIBRIL / protofilament | ||||||||||||
Function / homology | Function and homology information negative regulation of protein serine/threonine phosphatase activity / seedling development / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / response to salt stress / signaling receptor activity ...negative regulation of protein serine/threonine phosphatase activity / seedling development / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / response to salt stress / signaling receptor activity / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / Resolution: 1.351 Å | ||||||||||||
Model details | Protofilament structure of OsPYL/RCAR5 peptide determined by nanoEDT | ||||||||||||
Authors | Gallagher-Jones, M. / Richards, L.S. / Lee, S. / Rodriguez, J.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: IUCrJ / Year: 2020 Title: Atomic structures determined from digitally defined nanocrystalline regions. Authors: Marcus Gallagher-Jones / Karen C Bustillo / Colin Ophus / Logan S Richards / Jim Ciston / Sangho Lee / Andrew M Minor / Jose A Rodriguez / Abstract: Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm ...Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6uop.cif.gz | 10.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uop.ent.gz | 4.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uop_validation.pdf.gz | 401.4 KB | Display | wwPDB validaton report |
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Full document | 6uop_full_validation.pdf.gz | 401 KB | Display | |
Data in XML | 6uop_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6uop_validation.cif.gz | 2.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/6uop ftp://data.pdbj.org/pub/pdb/validation_reports/uo/6uop | HTTPS FTP |
-Related structure data
Related structure data | 6uoqC 6uorC 6uosC 6uouC 6uowC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 458.509 Da / Num. of mol.: 1 / Fragment: UNP residues 24-29 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice) / References: UniProt: Q6I5C3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Crystalline assembly of OsPYL/RCAR5 peptide derived from residues 24 - 29 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Oryza sativa (Asian cultivated rice) |
Buffer solution | pH: 7 |
Buffer component | Conc.: 10 % v/v / Name: Ethanol / Formula: C2H6O |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade |
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% ethanol |
-Data collection
Microscopy | Model: FEI TITAN | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER | ||||||||||||||||||||||||||||||||||||||||||||||||||
Electron lens | Mode: DIFFRACTION / Calibrated defocus min: 200 nm / Calibrated defocus max: 0 nm / C2 aperture diameter: 5 µm / Alignment procedure: OTHER | ||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 110 K / Temperature (min): 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Image recording | Average exposure time: 0.025 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K2 IS (4k x 4k) / Num. of diffraction images: 2496 / Num. of grids imaged: 1 / Num. of real images: 2496 Details: Images were collected in diffraction mode at 400 frames per second. | ||||||||||||||||||||||||||||||||||||||||||||||||||
EM imaging optics | Spherical aberration corrector: The TEAM1 microscope is double aberration-corrected. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Image scans | Sampling size: 10 µm / Width: 3840 / Height: 3520 | ||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction | Camera length: 510 mm | ||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction shell | Resolution: 1.351→5.75 Å / Fourier space coverage: 68.6 % / Multiplicity: 4.9 / Num. of structure factors: 405 / Phase residual: 1 ° | ||||||||||||||||||||||||||||||||||||||||||||||||||
EM diffraction stats | Fourier space coverage: 68.6 % / High resolution: 1.351 Å / Num. of intensities measured: 1981 / Num. of structure factors: 405 / Phase error: 33.04 ° / Phase residual: 1 ° / Phase error rejection criteria: None / Rmerge: 0.193 / Rsym: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction source | Source: ELECTRON MICROSCOPE / Type: TEAM1 / Wavelength: 0.0197 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: K2 IS / Detector: CMOS CAMERA / Date: Apr 4, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.0197 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→5.745 Å / Num. obs: 405 / % possible obs: 68.6 % / Redundancy: 4.891 % / Biso Wilson estimate: 15.747 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.215 / Χ2: 0.735 / Net I/σ(I): 3.77 / Num. measured all: 1981 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 4.71 Å / B: 11.49 Å / C: 38.9 Å / Space group name: P212121 / Space group num: 19 | ||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||
3D reconstruction | Resolution: 1.351 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||
Atomic model building | B value: 10.07 / Protocol: AB INITIO MODEL / Space: RECIPROCAL | ||||||||||||||||
Refinement | Resolution: 1.351→5.745 Å / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 33.04 / Stereochemistry target values: LS_WUNIT_K1
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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 max: 25.12 Å2 / Biso mean: 10.6411 Å2 / Biso min: 1.68 Å2 | ||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→5.74 Å /
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LS refinement shell | Resolution: 1.351→5.745 Å / Rfactor Rfree error: 0
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