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- PDB-6b1q: Hydrogen Bonding Complementary, not size complementarity is key i... -

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Basic information

Entry
Database: PDB / ID: 6b1q
TitleHydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix
Components
  • DNA (5'-D(*CP*TP*TP*AP*TP*(CJ1)P*(CJ1)P*(CJ1))-3')
  • DNA (5'-D(P*(1AP)P*(1AP)P*(1AP)P*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 / telomerase 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 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
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 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.3Oct 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: DNA (5'-D(*CP*TP*TP*AP*TP*(CJ1)P*(CJ1)P*(CJ1))-3')
G: DNA (5'-D(P*(1AP)P*(1AP)P*(1AP)P*AP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)34,3183
Polymers34,3183
Non-polymers00
Water4,936274
1
A: Reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*AP*TP*(CJ1)P*(CJ1)P*(CJ1))-3')
G: DNA (5'-D(P*(1AP)P*(1AP)P*(1AP)P*AP*TP*AP*AP*G)-3')

A: Reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*AP*TP*(CJ1)P*(CJ1)P*(CJ1))-3')
G: DNA (5'-D(P*(1AP)P*(1AP)P*(1AP)P*AP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)68,6366
Polymers68,6366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)55.278, 146.282, 46.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Reverse transcriptase


Mass: 29347.754 Da / Num. of mol.: 1 / 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*(CJ1)P*(CJ1)P*(CJ1))-3')


Mass: 2457.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*(1AP)P*(1AP)P*(1AP)P*AP*TP*AP*AP*G)-3')


Mass: 2512.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
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: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.896→146.282 Å / Num. obs: 31032 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Rsym value: 0.088 / Net I/av σ(I): 6.7 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-26.90.471.6303530.2080.5510.4799.6
2-2.1270.3142.40.1370.3660.31499.8
2.12-2.277.10.2323.30.10.270.23299.8
2.27-2.457.20.1654.60.0710.1930.16599.9
2.45-2.687.20.12360.0530.1430.123100
2.68-37.20.0927.70.040.1080.092100
3-3.467.10.0649.80.0280.0750.064100
3.46-4.2470.05211.80.0230.0620.052100
4.24-5.996.90.048120.0210.0560.048100
5.99-146.2826.20.04412.10.0210.0530.04498.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREPphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO0

4xo0


Resolution: 1.9→44.696 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2374 1535 4.99 %
Rwork0.2043 --
obs0.206 30765 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.05 Å2 / Biso mean: 31.3501 Å2 / Biso min: 9.24 Å2
Refinement stepCycle: final / Resolution: 1.9→44.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 334 0 274 2553
Biso mean---31.35 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082450
X-RAY DIFFRACTIONf_angle_d1.0343408
X-RAY DIFFRACTIONf_chiral_restr0.06368
X-RAY DIFFRACTIONf_plane_restr0.007385
X-RAY DIFFRACTIONf_dihedral_angle_d15.7331380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.96140.33431160.245726212737100
1.9614-2.03150.25221320.214425972729100
2.0315-2.11280.2411170.212326222739100
2.1128-2.2090.22411310.210626412772100
2.209-2.32540.24361400.212326232763100
2.3254-2.47110.24841500.206926212771100
2.4711-2.66190.25371420.20626492791100
2.6619-2.92970.25311560.218826592815100
2.9297-3.35350.25291400.205426642804100
3.3535-4.22460.20761480.192727142862100
4.2246-44.70850.22651630.19142819298299

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