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- PDB-7lem: Crystal structure of the first bromodomain (BD1) of human BRDT bo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lem | ||||||
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Title | Crystal structure of the first bromodomain (BD1) of human BRDT bound to LRRK2-IN-1 | ||||||
![]() | Bromodomain testis-specific protein | ||||||
![]() | GENE REGULATION / Bromodomain / LRRK / kinase | ||||||
Function / homology | ![]() sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chan, A. / Karim, M.R. / Schonbrunn, E. | ||||||
![]() | ![]() Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.2 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v67C ![]() 5vboC ![]() 5vbpC ![]() 5vbqC ![]() 5vbrC ![]() 7bjyC ![]() 7k6gC ![]() 7k6hC ![]() 7ko0C ![]() 7l6dC ![]() 7l72C ![]() 7l73SC ![]() 7l9gC ![]() 7l9jC ![]() 7l9kC ![]() 7l9lC ![]() 7lahC ![]() 7laiC ![]() 7lajC ![]() 7lakC ![]() 7lauC ![]() 7layC ![]() 7lazC ![]() 7lb4C ![]() 7lbtC ![]() 7lejC ![]() 7lekC ![]() 7lelC 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: 13319.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #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: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate trihydrate (pH 6.5), and 30 % w/v PEG 8,000 |
-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 20, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→35.25 Å / Num. obs: 23495 / % possible obs: 98.7 % / Redundancy: 3.645 % / Biso Wilson estimate: 34.851 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.051 / Χ2: 1.021 / Net I/σ(I): 17.14 / Num. measured all: 85628 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7L73 Resolution: 1.89→35.25 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.52 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.96 Å2 / Biso mean: 44.6938 Å2 / Biso min: 18.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→35.25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -8.1012 Å / Origin y: -2.6173 Å / Origin z: -21.4932 Å
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Refinement TLS group |
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