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- PDB-5l98: Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l98 | |||||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 4 | |||||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | |||||||||
![]() | TRANSCRIPTION / four helical bundle | |||||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lolli, G. / Marchand, J.-R. / Caflisch, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation. Authors: Marchand, J.R. / Lolli, G. / Caflisch, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.1 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.3 KB | Display | ![]() |
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Full document | ![]() | 730.3 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l8tC ![]() 5l8uC ![]() 5l96C ![]() 5l97C ![]() 5l99C ![]() 4ir5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-6RY / ~{ | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.22 % / Mosaicity: 0.32 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.26→48.2 Å / Num. obs: 10776 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Net I/σ(I): 17 / Num. measured all: 66170 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4IR5 Resolution: 2.263→48.197 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.1 Å2 / Biso mean: 57.7666 Å2 / Biso min: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.263→48.197 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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