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Yorodumi- PDB-6dbc: Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dbc | ||||||
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Title | Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue | ||||||
Components | Bromodomain-containing protein 2 | ||||||
Keywords | Transcription/inhibitor / BET / BRD2 / bromodomain / Inhibitor / Complex / Transcription / Transcription-inhibitor complex | ||||||
Function / homology | Function and homology information acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | White, S.W. / Yun, M. | ||||||
Citation | Journal: To Be Published Title: Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue Authors: White, S.W. / Yun, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dbc.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dbc.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dbc_validation.pdf.gz | 806.4 KB | Display | wwPDB validaton report |
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Full document | 6dbc_full_validation.pdf.gz | 806.4 KB | Display | |
Data in XML | 6dbc_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6dbc_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/6dbc ftp://data.pdbj.org/pub/pdb/validation_reports/db/6dbc | HTTPS FTP |
-Related structure data
Related structure data | 5ig6S 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: 13524.474 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25440 | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-G3J / | #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: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, Potassium thicyanate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 26, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→50 Å / Num. obs: 57487 / % possible obs: 99.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 8.97 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 1.083 / Net I/σ(I): 35.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IG6 Resolution: 1.05→29.723 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 10.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.98 Å2 / Biso mean: 14.4188 Å2 / Biso min: 6.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.05→29.723 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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