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Yorodumi- PDB-5czg: Crystal Structure Analysis of hypothetical bromodomain Tb427.10.7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5czg | ||||||
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Title | Crystal Structure Analysis of hypothetical bromodomain Tb427.10.7420 from Trypanosoma brucei in complex with bromosporine | ||||||
Components | Hypothetical Bromodomain | ||||||
Keywords | GENE REGULATION / Structural Genomics Consortium / SGC / Hypothetical bromodomain / Bromosporine | ||||||
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 brucei gambiense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å | ||||||
Authors | Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal Structure Analysis of hypothetical bromodomain from Trypanosoma brucei Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5czg.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5czg.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 5czg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/5czg ftp://data.pdbj.org/pub/pdb/validation_reports/cz/5czg | HTTPS FTP |
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-Related structure data
Related structure data | 5ameS 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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Details | The assembly of the structure is not examined in this experiment |
-Components
#1: Protein | Mass: 13206.827 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-115 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_X9100 / Plasmid: CodLnt RIL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0A3H5 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BMF / | #4: Chemical | ChemComp-UNX / #5: 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: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5M Sodium Citrate, 62.5 mM Tris-HC |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. obs: 20807 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 13.44 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Χ2: 2.195 / Net I/av σ(I): 52.026 / Net I/σ(I): 18.7 / Num. measured all: 152445 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AME Resolution: 1.451→36.766 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.12 / 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: 69.34 Å2 / Biso mean: 17.0854 Å2 / Biso min: 6.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.451→36.766 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
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