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- PDB-3a01: Crystal structure of Aristaless and Clawless homeodomains bound to DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a01 | ||||||
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Title | Crystal structure of Aristaless and Clawless homeodomains bound to DNA | ||||||
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![]() | Gene Regulation/DNA / HOMEODOMAIN / PROTEIN-DNA COMPLEX / DNA-binding / Homeobox / Nucleus / Developmental protein / Gene Regulation-DNA COMPLEX | ||||||
Function / homology | ![]() elongation of arista core / leg disc development / antennal morphogenesis / imaginal disc-derived leg morphogenesis / chaeta development / animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...elongation of arista core / leg disc development / antennal morphogenesis / imaginal disc-derived leg morphogenesis / chaeta development / animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miyazono, K. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M. | ||||||
![]() | ![]() Title: Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless Authors: Miyazono, K. / Zhi, Y. / Takamura, Y. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, 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 | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.7 KB | Display | ![]() |
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Full document | ![]() | 494.2 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a02SC ![]() 3a03SC ![]() 3lnqC ![]() 1pufS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 11191.974 Da / Num. of mol.: 2 / Fragment: Clawless Homeobox, residues 170-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 8335.609 Da / Num. of mol.: 2 / Fragment: Homeobox, residues 80-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: DNA chain | Mass: 5257.419 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: DNA chain | Mass: 5155.375 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.06 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 18995 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3A02, 3A03, and 1PUF Resolution: 2.7→19.65 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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