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Yorodumi- PDB-6nim: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nim | ||||||
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Title | Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine | ||||||
Components | Bromodomain factor 2 protein | ||||||
Keywords | SIGNALING PROTEIN / TcCLB.506553.20 / BDF2 / bromosporine / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Lin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine Authors: Lin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / 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 | 6nim.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nim.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nim_validation.pdf.gz | 750.8 KB | Display | wwPDB validaton report |
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Full document | 6nim_full_validation.pdf.gz | 751.2 KB | Display | |
Data in XML | 6nim_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6nim_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nim ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nim | HTTPS FTP |
-Related structure data
Related structure data | 5czgS 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: 13618.282 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_57g96 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE2 / References: UniProt: A0A2V2V5V1 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-UNX / #4: Chemical | ChemComp-BMF / | #5: 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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0.985 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M NH4SO4 and 0.1M bis Tris pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 22, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→50 Å / Num. obs: 23959 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.03 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 11.3 / Num. measured all: 91630 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CZG Resolution: 1.78→21.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.561 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.08 Å2 / Biso mean: 23.223 Å2 / Biso min: 14.41 Å2
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Refinement step | Cycle: final / Resolution: 1.78→21.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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