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Yorodumi- PDB-6b1s: Hydrogen Bonding Complementary, not size complementarity is key i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b1s | ||||||
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Title | Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Protein-DNA / AEGIS / unnatural base pair / host-guest system / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Singh, I. / Georgiadis, M.M. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: "Skinny" and "Fat" DNA: Two New Double Helices. Authors: Hoshika, S. / Singh, I. / Switzer, C. / Molt Jr., R.W. / Leal, N.A. / Kim, M.J. / Kim, M.S. / Kim, H.J. / Georgiadis, M.M. / Benner, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b1s.cif.gz | 347.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b1s.ent.gz | 286.9 KB | Display | PDB format |
PDBx/mmJSON format | 6b1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b1s_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 6b1s_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 6b1s_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 6b1s_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b1s ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b1s | HTTPS FTP |
-Related structure data
Related structure data | 6b1qC 6b1rC 4xo0S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 29347.754 Da / Num. of mol.: 2 / Fragment: Catalytic fragment (UNP residues 683-937) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase #2: DNA chain | Mass: 4937.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: 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: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6 % 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: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→35.68 Å / Num. obs: 50699 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.72 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.046 / Rrim(I) all: 0.125 / Net I/σ(I): 14.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XO0 Resolution: 2→14.742 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→14.742 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -25.4365 Å / Origin y: 19.6976 Å / Origin z: 181.3079 Å
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Refinement TLS group | Selection details: all |