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Yorodumi- PDB-4q0o: Crystal Structure of the fifth bromodomain of Human Poly-bromodom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q0o | ||||||
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Title | Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | TRANSCRIPTION / PB1 / POLYBROMO 1 ISOFORM 1 / BAF180 / POLYBROMO-1D / PBRM1 / BRG1-ASSOCIATED FACTOR 180 / BROMODOMAIN / CHROMATIN REGULATOR / DNA-BINDING / NUCLEUS / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand Authors: Filippakopoulos, P. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q0o.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q0o.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/4q0o ftp://data.pdbj.org/pub/pdb/validation_reports/q0/4q0o | HTTPS FTP |
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-Related structure data
Related structure data | 4q0nC 3mb4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14648.000 Da / Num. of mol.: 1 / Fragment: UNP residues 645-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAF180, PB1, PBRM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86 |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-2XC / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.20M K3(cit), 0.1M BTProp pH 6.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.7 % / Number: 89732 / Rsym value: 0.054 / D res high: 1.83 Å / D res low: 29.605 Å / Num. obs: 15658 / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.83→29.605 Å / Num. all: 15674 / Num. obs: 15658 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 16.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MB4 Resolution: 1.83→29.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2188 / WRfactor Rwork: 0.1877 / FOM work R set: 0.8569 / SU B: 4.884 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1158 / SU Rfree: 0.1113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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: 144.25 Å2 / Biso mean: 38.03 Å2 / Biso min: 18.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -11.6969 Å / Origin y: -21.4272 Å / Origin z: -4.7329 Å
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