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Yorodumi- PDB-2r2u: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r2u | ||||||
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Title | Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment | ||||||
Components |
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Keywords | transferase/DNA / bleomycin / drug-DNA complex / protein-DNA complex / MMLV RT / Aspartyl protease / DNA integration / DNA recombination / Endonuclease / Hydrolase / Multifunctional enzyme / Nuclease / Nucleotidyltransferase / Protease / RNA-directed DNA polymerase / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...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 / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 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 / Resolution: 2.3 Å | ||||||
Authors | Goodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding. Authors: Goodwin, K.D. / Lewis, M.A. / 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 | 2r2u.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r2u.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/2r2u ftp://data.pdbj.org/pub/pdb/validation_reports/r2/2r2u | HTTPS FTP |
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-Related structure data
Related structure data | 2r2rC 2r2sC 2r2tC 1ztwS C: citing same article (ref.) 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 | The biological assembly is equivalent to 15 base pairs of DNA intercalated by two molecules of BLM with one molecule of MMLV RT bound on each end of the DNA. Symmetry is generated from the asymmetric unit by the operations: x, y, z and 2-x, 1-y, z. |
-Components
#1: DNA chain | Mass: 2127.433 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2409.630 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: residues 144-398 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase |
#4: Chemical | ChemComp-BTZ / |
#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: 2.85 Å3/Da / Density % sol: 56.9 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.068828 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.068828 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 16721 / % possible obs: 96.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.072 / Χ2: 1.006 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZTW Resolution: 2.3→30 Å / σ(F): 0
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Solvent computation | Bsol: 36.896 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.152 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Xplor file |
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