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Yorodumi- PDB-5tck: Second Bromodomain from Leishmania donovani LdBPK.091320 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tck | ||||||
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Title | Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Bromodomain / Structural Genomics Consortium (SGC) | ||||||
Function / homology | Function and homology information lysine-acetylated histone binding / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Lin, L.-H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine Authors: Lin, L.-H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.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 | 5tck.cif.gz | 223.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tck.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 5tck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/5tck ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tck | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17959.279 Da / Num. of mol.: 2 / Fragment: UNP residues 161-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote) Strain: BPK282A1 / Gene: LDBPK_091320 / Plasmid: pET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: E9BA17 |
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-Non-polymers , 5 types, 179 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 1.88 Å3/Da / Density % sol: 34.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The protein was crystallized at 293 K with 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350 with Bromosporine using the sitting drop method. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 20521 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 36.86 Å2 / Net I/σ(I): 24.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→26.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.161
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Displacement parameters | Biso mean: 39.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→26.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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