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Open data
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Basic information
Entry | Database: PDB / ID: 7smd | ||||||
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Title | p107 pocket domain complexed with EID1 peptide | ||||||
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Function / homology | ![]() histone acetyltransferase regulator activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Putta, S. / Fernandez, S.M. / Tripathi, S.M. / Muller, G.A. / Rubin, S.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Authors: Putta, S. / Alvarez, L. / Ludtke, S. / Sehr, P. / Muller, G.A. / Fernandez, S.M. / Tripathi, S. / Lewis, J. / Gibson, T.J. / Chemes, L.B. / Rubin, S.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 | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7smcC ![]() 7smeC ![]() 7smfC ![]() 4yosS 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: 43265.965 Da / Num. of mol.: 1 / Fragment: UNP residues 391-601,780-887,924-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1635.769 Da / Num. of mol.: 1 / Fragment: UNP residues 174-187 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→33.92 Å / Num. obs: 27480 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.15→2.22 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.69 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4YOS Resolution: 2.15→33.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.47 / 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: 2.15→33.92 Å
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Refine LS restraints |
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LS refinement shell |
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