+
Open data
-
Basic information
Entry | Database: PDB / ID: 4lc2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the bromodomain of human BRPF1B | ||||||
![]() | Peregrin | ||||||
![]() | DNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1 / Protein Br140 / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structure of the bromodomain of human BRPF1B Authors: Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, H.C. / Edwards, M.A. / Bountra, C. / Knapp, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 64.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dvvS ![]() 1x0jS ![]() 2grcS ![]() 2oo1S ![]() 2ossS ![]() 2ouoS ![]() 3d7cS ![]() 3daiS ![]() 3dwyS ![]() 3hmhS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 1 / Fragment: unp residues 626-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NO3 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 20% PEG3350 0.1 M bis tris propane, 10% ethylene glycol 0.15 M sodium nitrate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→19 Å / Num. all: 16843 / Num. obs: 16793 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 40.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 55.63 / Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY Resolution: 1.65→19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2241 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8648 / SU B: 3.331 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0901 / SU Rfree: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.16 Å2 / Biso mean: 25.5295 Å2 / Biso min: 8.91 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 12.7879 Å / Origin y: 25.2852 Å / Origin z: 11.1287 Å
|