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- PDB-6nez: Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nez | ||||||
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Title | Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1 | ||||||
![]() | Uncharacterized protein | ||||||
![]() | TRANSCRIPTION / Tb427tmp / PF-CBP1 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | lysine-acetylated histone binding / Bromodomain / Bromodomain / Bromodomain-like superfamily / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / Chem-KJS / Bromo domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. ...Lin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R.J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1 Authors: Lin, Y.H. / Dong, A. / Tempel, W. / McAuley, J. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Harding, R.J. / Structural Genomics Consortium (SGC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k29S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14063.993 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb11.01.5000 / Plasmid: pET15-MHL / Production host: ![]() ![]() #2: Chemical | ChemComp-KJS / #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.34 % / Mosaicity: 1.028 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.27 M Na Formate, and 0.1M Na Acetate pH4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 35904 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.037 / Rrim(I) all: 0.106 / Χ2: 0.957 / Net I/σ(I): 6.3 / Num. measured all: 286191 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5K29 Resolution: 2.2→42.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.422 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 107.12 Å2 / Biso mean: 42.996 Å2 / Biso min: 28.69 Å2
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Refinement step | Cycle: final / Resolution: 2.2→42.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.198→2.255 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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