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- PDB-3k2j: Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k2j | ||||||
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Title | Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) | ||||||
![]() | Protein polybromo-1 | ||||||
![]() | TRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo01D / PBRM1 / BRG1-associated factor 180 / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) Authors: Filippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.4 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbS ![]() 2oo1S ![]() 2ossS ![]() 2ouoS ![]() 2rfjS ![]() 3d7cS ![]() 3daiS ![]() 3dwyS 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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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 346 - 459 / Label seq-ID: 14 - 127
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Details | The protein is monomeric by gel filtration. |
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Components
#1: Protein | Mass: 15619.836 Da / Num. of mol.: 2 / Fragment: Bromo 3 domain, UNP residues 388-494 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % / Mosaicity: 0.23 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M NaOAc.3H20 pH 5.5, 1.1M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36.221 Å / Num. all: 15266 / Num. obs: 15266 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2 / Num. unique all: 2231 / Rsym value: 0.744 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 35.59 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY Resolution: 2.2→36.22 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.278 / WRfactor Rwork: 0.233 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.799 / SU B: 16.939 / SU ML: 0.191 / SU R Cruickshank DPI: 0.281 / SU Rfree: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.22 Å2 / Biso mean: 33.606 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→36.22 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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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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