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Yorodumi- PDB-4nrb: Crystal Structure of the bromodomain of human BAZ2B in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nrb | ||||||
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Title | Crystal Structure of the bromodomain of human BAZ2B in complex with compound-1 N01197 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / SGC / Structural Genomics Consortium / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4 | ||||||
Function / homology | Function and homology information chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Muniz, J.R.C. / Felletar, I. / Chaikuad, A. / Filippakopoulos, P. / Ferguson, F.M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Muniz, J.R.C. / Felletar, I. / Chaikuad, A. / Filippakopoulos, P. / Ferguson, F.M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Ciulli, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. Authors: Ferguson, F.M. / Fedorov, O. / Chaikuad, A. / Philpott, M. / Muniz, J.R. / Felletar, I. / von Delft, F. / Heightman, T. / Knapp, S. / Abell, C. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nrb.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nrb.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nrb_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 4nrb_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 4nrb_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4nrb_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/4nrb ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nrb | HTTPS FTP |
-Related structure data
Related structure data | 4nr9C 4nraC 4nrcC 3g0lS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9UIF8 |
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#2: Chemical | ChemComp-2LX / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Sequence details | THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.45 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 19% PEG 1000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 30, 2011 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→29.93 Å / Num. all: 14018 / Num. obs: 14004 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2 / Num. unique all: 2004 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3G0L Resolution: 2.08→28.84 Å / Cor.coef. Fo:Fc: 0.9381 / Cor.coef. Fo:Fc free: 0.9178 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
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Displacement parameters | Biso mean: 30.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.237 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→28.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.25 Å / Total num. of bins used: 7
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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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