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Yorodumi- PDB-5fh8: Crystal structure of the fifth bromodomain of human PB1 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fh8 | ||||||
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Title | Crystal structure of the fifth bromodomain of human PB1 in complex with compound 28 | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | TRANSCRIPTION / PBRM1 / BRG1-associated factor 180 / chromatin remodeling | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Tallant, C. / Sutherell, C.L. / Siejka, P. / Sorrell, F.J. / Krojer, T. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Sutherell, C.L. / Siejka, P. / Sorrell, F.J. / Krojer, T. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Ley, S.V. / Knapp, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex. Authors: Sutherell, C.L. / Tallant, C. / Monteiro, O.P. / Yapp, C. / Fuchs, J.E. / Fedorov, O. / Siejka, P. / Muller, S. / Knapp, S. / Brenton, J.D. / Brennan, P.E. / Ley, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fh8.cif.gz | 198.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fh8.ent.gz | 159.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fh8_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5fh8_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5fh8_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5fh8_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fh8 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fh8 | HTTPS FTP |
-Related structure data
Related structure data | 5fh6C 5fh7C 4q0oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14648.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86 #2: Chemical | ChemComp-5XK / #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% MPD, 0.1 M bicine pH 9 / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→64.55 Å / Num. all: 68763 / Num. obs: 68763 / % possible obs: 90.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.55→6.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.5 / % possible all: 52.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q0O Resolution: 1.55→64.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.376 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→64.55 Å
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Refine LS restraints |
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