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Yorodumi- PDB-8qtc: Crystal structure of Arabidopsis thaliana 14-3-3 omega in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qtc | ||||||
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Title | Crystal structure of Arabidopsis thaliana 14-3-3 omega in complex with a phosphopeptide from the transcription factor BZR1. | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 14-3-3 / brassinosteroid / transcription factor / BZR1 / phosphopeptide / signal transduction / plant growth | ||||||
Function / homology | Function and homology information brassinosteroid mediated signaling pathway / plant-type vacuole / Golgi apparatus / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Hothorn, M. / Obergfell, E. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Plant Cell.Physiol. / Year: 2024 Title: Mechanistic insights into the function of 14-3-3 proteins as negative regulators of brassinosteroid signaling in Arabidopsis. Authors: Obergfell, E. / Hohmann, U. / Moretti, A. / Chen, H. / Hothorn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qtc.cif.gz | 244.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qtc.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/8qtc ftp://data.pdbj.org/pub/pdb/validation_reports/qt/8qtc | HTTPS FTP |
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-Related structure data
Related structure data | 8qt5C 8qtfC 8qttC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 235 / Label seq-ID: 3 - 235
NCS oper: (Code: givenMatrix: (-0.757960476169, -0.649309709613, 0.0623924480031), (-0.649173983086, 0.741515285845, -0.169494013292), (0.063789154636, -0.168973317007, -0.983554249592)Vector: -4. ...NCS oper: (Code: given Matrix: (-0.757960476169, -0.649309709613, 0.0623924480031), Vector: |
-Components
#1: Protein | Mass: 27171.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: GRF2 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: Q01525 #2: Protein/peptide | | Mass: 554.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: BZR1 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL #3: Chemical | ChemComp-CO / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 M (NH4)2SO4 , 10 mM CoCl2 6 H2O, 0.1 M Mes (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999999406361 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999999406361 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→68.35 Å / Num. obs: 17253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 38.3 % / Biso Wilson estimate: 142.23 Å2 / CC1/2: 1 / Rrim(I) all: 0.339 / Net I/σ(I): 14.32 |
Reflection shell | Resolution: 3.5→3.71 Å / Redundancy: 39.6 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 2692 / CC1/2: 0.37 / Rrim(I) all: 5.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→68.35 Å / SU ML: 0.5213 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9986 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 158.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→68.35 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.3338746232 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.1484139794 Å / Origin y: -48.6865558576 Å / Origin z: -25.9408263021 Å
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Refinement TLS group | Selection details: all |