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- PDB-6b1s: Hydrogen Bonding Complementary, not size complementarity is key i... -

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Basic information

Entry
Database: PDB / ID: 6b1s
TitleHydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix
Components
  • DNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')
  • Reverse transcriptase
KeywordsDNA 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 / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, I. / Georgiadis, M.M.
CitationJournal: 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
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation_author
Item: _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase
B: Reverse transcriptase
E: DNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')
F: DNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)68,5704
Polymers68,5704
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.119, 95.797, 144.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reverse transcriptase


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 DNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')


Mass: 4937.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.057.40.68837080.7930.270.74100
8.94-35.685.60.0590.970.0290.06690.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO0

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
RfactorNum. reflection% reflection
Rfree0.2513 2462 4.88 %
Rwork0.2166 --
obs0.2182 50488 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→14.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 654 0 265 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034770
X-RAY DIFFRACTIONf_angle_d0.7056630
X-RAY DIFFRACTIONf_dihedral_angle_d17.1242744
X-RAY DIFFRACTIONf_chiral_restr0.044733
X-RAY DIFFRACTIONf_plane_restr0.005749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03840.27451280.27472661X-RAY DIFFRACTION100
2.0384-2.07990.30361380.25352593X-RAY DIFFRACTION100
2.0799-2.1250.2631350.2492656X-RAY DIFFRACTION100
2.125-2.17430.27641380.24562623X-RAY DIFFRACTION100
2.1743-2.22840.27451490.24212639X-RAY DIFFRACTION100
2.2284-2.28850.28551510.24212623X-RAY DIFFRACTION100
2.2885-2.35560.26861400.22872618X-RAY DIFFRACTION100
2.3556-2.43130.29341430.22782652X-RAY DIFFRACTION100
2.4313-2.51780.24381510.22292649X-RAY DIFFRACTION100
2.5178-2.6180.26331160.21842652X-RAY DIFFRACTION100
2.618-2.73650.28291160.23132688X-RAY DIFFRACTION100
2.7365-2.87970.27891350.23042656X-RAY DIFFRACTION100
2.8797-3.05860.24711250.22892681X-RAY DIFFRACTION100
3.0586-3.29240.26771210.23092702X-RAY DIFFRACTION100
3.2924-3.61930.26061330.2172693X-RAY DIFFRACTION100
3.6193-4.13280.27611430.20022720X-RAY DIFFRACTION100
4.1328-5.16940.17061470.17342721X-RAY DIFFRACTION100
5.1694-14.74230.2351530.22799X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -25.4365 Å / Origin y: 19.6976 Å / Origin z: 181.3079 Å
111213212223313233
T0.2103 Å20.0303 Å20.0476 Å2-0.2323 Å2-0.0381 Å2--0.192 Å2
L0.6795 °20.2108 °20.9066 °2-0.2163 °20.1524 °2--0.9629 °2
S0.0247 Å °0.0902 Å °-0.1277 Å °-0.0535 Å °0.0496 Å °-0.0085 Å °0.0817 Å °0.1009 Å °-0.0515 Å °
Refinement TLS groupSelection details: all

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