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Yorodumi- PDB-3fsi: Crystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fsi | ||||||
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Title | Crystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)diphenylamine bound to DNA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE/DNA MMLV RT / PROTEIN-DNA COMPLEX / DRUG-DNA COMPLEX / CD27 / antitrypanosomal / DNA integration / DNA recombination / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Glass, L.S. / Georgiadis, M.M. / Goodwin, K.D. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA. Authors: Glass, L.S. / Nguyen, B. / Goodwin, K.D. / Dardonville, C. / Wilson, W.D. / Long, E.C. / Georgiadis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fsi.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fsi.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fsi_validation.pdf.gz | 652.5 KB | Display | wwPDB validaton report |
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Full document | 3fsi_full_validation.pdf.gz | 658.5 KB | Display | |
Data in XML | 3fsi_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3fsi_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/3fsi ftp://data.pdbj.org/pub/pdb/validation_reports/fs/3fsi | HTTPS FTP |
-Related structure data
Related structure data | 1ztwS 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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Details | Two protein molecules joined by a 16mer-bp double strand of DNA, with CD27 bound to both 5'-AATT sites. One asymmetric unit retains one half of the 16mer-bp, one protein and one bound ligand. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28934.287 Da / Num. of mol.: 1 Fragment: Reverse transcriptase domain: UNP residues 144-398 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Gene: MoMLV, pol / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P03355, RNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules GB
#2: DNA chain | Mass: 2376.591 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2474.667 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 234 molecules
#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-MWB / | #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: 2.7 Å3/Da / Density % sol: 54.51 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, Magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008001 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2006 Details: Rosenbaum-Rock vertical focusing mirror, LN2 cooled first crystal, sagital focusing 2nd crystal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.008001 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 35935 / % possible obs: 95 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.045 / Χ2: 1.037 / Net I/σ(I): 24.677 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZTW Resolution: 1.75→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / σ(F): 0
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Solvent computation | Bsol: 52.54 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.37 Å2 / Biso mean: 32.116 Å2 / Biso min: 13.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.8 Å / Num. reflection obs: 3510 | ||||||||||||||||||||||||||||
Xplor file |
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