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Yorodumi- PDB-3svf: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3svf | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with a dihydro-quinazolin ligand | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | UNKNOWN FUNCTION / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-WDR / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.975 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the first bromodomain of human BRD4 in complex with a dihydro-quinazolin ligand Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3svf.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3svf.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 3svf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3svf_validation.pdf.gz | 775.4 KB | Display | wwPDB validaton report |
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Full document | 3svf_full_validation.pdf.gz | 775.3 KB | Display | |
Data in XML | 3svf_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3svf_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/3svf ftp://data.pdbj.org/pub/pdb/validation_reports/sv/3svf | HTTPS FTP |
-Related structure data
Related structure data | 2ossS 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: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O60885 |
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#2: Chemical | ChemComp-WDR / ( |
#3: 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: 2.13 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Na(OAc), 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 8.5, 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: Jun 26, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.5 % / Av σ(I) over netI: 4 / Number: 60901 / Rsym value: 0.185 / D res high: 1.975 Å / D res low: 28.641 Å / Num. obs: 9376 / % possible obs: 98.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.975→28.641 Å / Num. all: 9490 / Num. obs: 9376 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.185 / Rsym value: 0.185 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 38.14 / 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 2OSS Resolution: 1.975→28.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.1561 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8696 / SU B: 7.758 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1873 / SU Rfree: 0.1656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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: 102.99 Å2 / Biso mean: 23.6867 Å2 / Biso min: 9.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.975→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.975→2.026 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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