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Yorodumi- PDB-5c8g: Crystal Structure Analysis of PP-BRD20 from Tb427tmp complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c8g | ||||||
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Title | Crystal Structure Analysis of PP-BRD20 from Tb427tmp complexed with BI-2536 | ||||||
Components | PP-BRD20 | ||||||
Keywords | GENE REGULATION / Structural Genomics Consortium / SGC / Bromodomain / PP-BRD20 / Tb427tmp | ||||||
Function / homology | Function and homology information Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Trypanosoma brucei gambiense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. ...Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amain, M. / Lin, Y.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal Structure Analysis of PP-BRD20 from Tb427tmp Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Hou, C.F.D. / El Bakkouri, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Lin, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c8g.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c8g.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8g ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8g | HTTPS FTP |
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-Related structure data
Related structure data | 4uygS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15870.821 Da / Num. of mol.: 2 / Fragment: UNP residues 25-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972) (eukaryote) Strain: MHOM/CI/86/DAL972 / Gene: TbgDal_XI11310 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0A8L1 #2: Chemical | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97957 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 20890 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.053 / Rrim(I) all: 0.118 / Χ2: 1.438 / Net I/av σ(I): 19.321 / Net I/σ(I): 6.8 / Num. measured all: 104944 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UYG Resolution: 1.95→30.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.14 / 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: 61.7 Å2 / Biso mean: 23.2579 Å2 / Biso min: 8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→30.38 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %
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