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Yorodumi- PDB-5orb: Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5orb | ||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å | ||||||
Authors | Lolli, G. / Dalle Vedove, A. / Marchand, J.-R. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J Chem Inf Model / Year: 2017 Title: Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Authors: Marchand, J.R. / Dalle Vedove, A. / Lolli, G. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5orb.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5orb.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 5orb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/5orb ftp://data.pdbj.org/pub/pdb/validation_reports/or/5orb | HTTPS FTP |
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-Related structure data
Related structure data | 5or8C 5or9C 5dyuS 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: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1858-1972 Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Details: First two residues SM derive from the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8 |
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#2: Chemical | ChemComp-JR6 / |
#3: Chemical | ChemComp-EDO / |
#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: 4.18 Å3/Da / Density % sol: 70.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.103→48.394 Å / Num. obs: 9775 / % possible obs: 72.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Net I/σ(I): 12.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DYU Resolution: 2.103→48.394 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81 Details: Data were strongly anisotropic. Data were subjected to ellipsoidal processing through the Staraniso server (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). As such, spherical ...Details: Data were strongly anisotropic. Data were subjected to ellipsoidal processing through the Staraniso server (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). As such, spherical completeness is low overall and in highest resolution shells. Included data contribute however relevantly to the density maps.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.53 Å2 / Biso mean: 31.9924 Å2 / Biso min: 8.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.103→48.394 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: 4
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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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