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Yorodumi- PDB-5c6q: Crystal structure of the apo TOPLESS related protein 2 (TPR2) N-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c6q | ||||||||||||
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Title | Crystal structure of the apo TOPLESS related protein 2 (TPR2) N-terminal domain (1-209) from rice | ||||||||||||
Components | ASPR2 protein | ||||||||||||
Keywords | TRANSCRIPTION / Transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / plant development | ||||||||||||
Function / homology | Function and homology information positive regulation of pattern recognition receptor signaling pathway / protein sequestering activity / regulation of DNA-templated transcription / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.251 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 | 5c6q.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c6q.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 5c6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c6q_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 5c6q_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 5c6q_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5c6q_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/5c6q ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c6q | HTTPS FTP |
-Related structure data
Related structure data | 4zheSC 5c6vC 5c7eC 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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Unit cell |
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-Components
#1: Protein | Mass: 24903.611 Da / Num. of mol.: 1 / 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M BIS-TRIS, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27821 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2014 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27821 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. all: 10544 / Num. obs: 10544 / % possible obs: 100 % / Redundancy: 15.3 % / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZHE Resolution: 3.251→34.71 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 32.18 / 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: 3.251→34.71 Å
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Refine LS restraints |
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LS refinement shell |
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