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- PDB-6to5: Crystal structure of the oligomerisation domain of the transcript... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6to5 | |||||||||
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Title | Crystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis. | |||||||||
![]() | Protein PHOSPHATE STARVATION RESPONSE 1 | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() response to arsenite ion / sulfate ion homeostasis / cellular response to high light intensity / cellular response to phosphate starvation / regulation of monoatomic ion transmembrane transport / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hothorn, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis. Authors: Ried, M.K. / Wild, R. / Zhu, J. / Pipercevic, J. / Sturm, K. / Broger, L. / Harmel, R.K. / Abriata, L.A. / Hothorn, L.A. / Fiedler, D. / Hiller, S. / Hothorn, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6to9C ![]() 6tocC ![]() 5iitS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9315.647 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.97 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M phosphate citrate pH 4.2, 0.2 M NaCl, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.38→47.18 Å / Num. obs: 16576 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 1 / Rrim(I) all: 0.189 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.38→2.52 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 2262 / CC1/2: 0.69 / Rrim(I) all: 2.21 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5IIT Resolution: 2.38→47.17 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0838
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→47.17 Å
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Refine LS restraints |
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LS refinement shell |
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