+Open data
-Basic information
Entry | Database: PDB / ID: 5vbs | ||||||
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Title | Structural basis for a six letter alphabet including GATCKX | ||||||
Components |
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Keywords | transferase/dna / Protein-DNA / AEGIS / unnatural base pair / host-guest system / transferase-dna complex | ||||||
Function / homology | Function and homology information retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.749 Å | ||||||
Authors | Singh, I. / Georgiadis, M.M. | ||||||
Citation | Journal: ACS Synth Biol / Year: 2017 Title: Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K). Authors: Singh, I. / Kim, M.J. / Molt, R.W. / Hoshika, S. / Benner, S.A. / 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 | 5vbs.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vbs.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/5vbs ftp://data.pdbj.org/pub/pdb/validation_reports/vb/5vbs | HTTPS FTP |
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-Related structure data
Related structure data | 1xo0S 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: 29347.754 Da / Num. of mol.: 1 / Fragment: unp residues 683-987 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus (isolate Shinnick) Strain: isolate Shinnick / Gene: gag-pol Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P03355, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
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#2: DNA chain | Mass: 2434.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#3: DNA chain | Mass: 2417.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#4: 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: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 6, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→100 Å / Num. obs: 38374 / % possible obs: 98.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Χ2: 0.899 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1XO0 Resolution: 1.749→33.722 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.57 Å2 / Biso mean: 27.3772 Å2 / Biso min: 8.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.749→33.722 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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