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Yorodumi- PDB-6toc: Crystal structure of the oligomerisation domain of the transcript... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6toc | |||||||||
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Title | Crystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis (crystal form 3). | |||||||||
Components | Protein PHOSPHATE STARVATION RESPONSE 1 | |||||||||
Keywords | TRANSCRIPTION / phosphate starvation / myb domain / coiled-coil domain / inositol pyrophosphate / plant nutrition | |||||||||
Function / homology | Function and homology information response to arsenite ion / sulfate ion homeostasis / cellular response to high light intensity / cellular response to phosphate starvation / regulation of monoatomic ion transmembrane transport / circadian rhythm / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å | |||||||||
Authors | Hothorn, M. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Nat Commun / Year: 2021 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. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6toc.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6toc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6toc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/6toc ftp://data.pdbj.org/pub/pdb/validation_reports/to/6toc | HTTPS FTP |
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-Related structure data
Related structure data | 6to5SC 6to9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3571040 / Data set type: diffraction image data / Metadata reference: 10.5281/zenodo.3571040 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
-Components
#1: Protein | Mass: 9372.700 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHR1, At4g28610, T5F17.60 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q94CL7 #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 grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tri pH 6.5, 0.1 M NaCl, 1.5 M (NH4)2SO4 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 5, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.85→31.523 Å / Num. obs: 6769 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / CC1/2: 1 / Rrim(I) all: 0.073 / Net I/σ(I): 21.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.85→1.97 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1072 / CC1/2: 0.4 / Rrim(I) all: 2.76 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TO5 Resolution: 1.853→31.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.66 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.037 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.853→31.5 Å
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Refine LS restraints |
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LS refinement shell |
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