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Yorodumi- PDB-5cq5: Crystal structure of the bromodomain of bromodomain adjacent to z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cq5 | ||||||
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Title | Crystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with 2,3-Ethylenedioxybenzoic Acid (SGC - Diamond I04-1 fragment screening) | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 1.961 Å | ||||||
Authors | Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be published Title: Crystal structure of the second bromodomain of bromodomain adjancent to zinc finger domain protein 2B (BAZ2B) in complex with 2,3-Ethylenedioxybenzoic Acid (SGC - Diamond I04-1 fragment screening) Authors: Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cq5.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cq5.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 5cq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cq5 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cq5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14057.129 Da / Num. of mol.: 1 / Fragment: Bromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8 | ||||
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#2: Chemical | #3: Chemical | #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: 4.1 Å3/Da / Density % sol: 69.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 25% PEG600 , 0.1M MES pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.96→29 Å / Num. obs: 16625 / % possible obs: 98.2 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.029 / Net I/σ(I): 18.8 / Num. measured all: 84050 / Scaling rejects: 1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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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 / Resolution: 1.961→19.642 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 75.83 Å2 / Biso mean: 33.1714 Å2 / Biso min: 17 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.961→19.642 Å
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