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Open data
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Basic information
Entry | Database: PDB / ID: 7to8 | ||||||
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Title | BRD3-BD1 in complex with RaPID linear peptide 2xAcK.1 (diAcK.1) | ||||||
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![]() | TRANSCRIPTION / BET / bromodomain / RaPID / BRD3 / acetylated | ||||||
Function / homology | ![]() lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patel, K. / Low, J.K.K. / Mackay, J.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome. Authors: Low, J.K.K. / Patel, K. / Jones, N. / Solomon, P. / Norman, A. / Maxwell, J.W.C. / Pachl, P. / Matthews, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Walport, L.J. / Mackay, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.5 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.1 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7to7C ![]() 7to9C ![]() 7toaC ![]() 3s91S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 15095.392 Da / Num. of mol.: 2 / Fragment: BD1 (UNP residues 25-147) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1751.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: 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: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, pH 6.0, 25% w/v PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.05 Å / Num. obs: 43909 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2114 / CC1/2: 0.94 / Rpim(I) all: 0.229 / Rrim(I) all: 0.438 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3S91 Resolution: 1.5→41.05 Å / SU ML: 0.1277 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5228 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.05 Å
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Refine LS restraints |
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LS refinement shell |
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