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Yorodumi- PDB-5c7e: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c7e | ||||||||||||
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Title | Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / Plant development | ||||||||||||
Function / homology | Function and homology information response to chitin / positive regulation of pattern recognition receptor signaling pathway / response to auxin / auxin-activated signaling pathway / protein sequestering activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Oryza sativa (Asian cultivated rice) Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Ke, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2015 Title: Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors. Authors: Ke, J. / Ma, H. / Gu, X. / Thelen, A. / Brunzelle, J.S. / Li, J. / Xu, H.E. / Melcher, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c7e.cif.gz | 267.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c7e.ent.gz | 217.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c7e_validation.pdf.gz | 519.4 KB | Display | wwPDB validaton report |
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Full document | 5c7e_full_validation.pdf.gz | 537.3 KB | Display | |
Data in XML | 5c7e_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 5c7e_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/5c7e ftp://data.pdbj.org/pub/pdb/validation_reports/c7/5c7e | HTTPS FTP |
-Related structure data
Related structure data | 4zheSC 5c6qC 5c6vC 5c7fC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24903.611 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 1-209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: P0705D01.10-1, ASPR2, Os01g0254100, OsJ_01134 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5NBT9 #2: Protein/peptide | Mass: 1160.273 Da / Num. of mol.: 6 / Fragment: UNP residues 41-51 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q38828 #3: Chemical | ChemComp-ZN / #4: 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: 4 Å3/Da / Density % sol: 69.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07818 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2014 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07818 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 44008 / Num. obs: 44008 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZHE Resolution: 3.1→44.995 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 26.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→44.995 Å
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Refine LS restraints |
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LS refinement shell |
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