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- PDB-6b1r: Hydrogen Bonding Complementary, not size complementarity is key i... -

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Basic information

Entry
Database: PDB / ID: 6b1r
TitleHydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix
Components
  • DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(1WA))-3')
  • DNA (5'-D(P*(IGU)P*(IGU)P*(IGU)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 / 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 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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*(1WA)P*(1WA)P*(1WA))-3')
G: DNA (5'-D(P*(IGU)P*(IGU)P*(IGU)P*AP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)34,3273
Polymers34,3273
Non-polymers00
Water3,963220
1
A: Reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(1WA))-3')
G: DNA (5'-D(P*(IGU)P*(IGU)P*(IGU)P*AP*TP*AP*AP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)68,6546
Polymers68,6546
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_475-x-1,-y+2,z1
Unit cell
Length a, b, c (Å)55.214, 146.194, 47.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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*(1WA)P*(1WA)P*(1WA))-3')


Mass: 2463.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*(IGU)P*(IGU)P*(IGU)P*AP*TP*AP*AP*G)-3')


Mass: 2515.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
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: 1.69→146.194 Å / Num. obs: 43517 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.41 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Rsym value: 0.066 / Net I/av σ(I): 7.3 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.691-1.786.50.6441.2275150.2950.7620.644100
1.78-1.896.70.4071.90.1830.4790.407100
1.89-2.026.80.2363.30.1060.2780.236100
2.02-2.186.90.1550.0660.1750.15100
2.18-2.397.10.10670.0470.1250.106100
2.39-2.677.20.07990.0340.0920.079100
2.67-3.097.20.0610.90.0260.070.06100
3.09-3.787.10.04712.40.0210.0550.047100
3.78-5.356.90.03914.80.0170.0470.039100
5.35-146.1946.30.03715.10.0180.0450.03796.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO0

4xo0


Resolution: 1.69→33.857 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2125 4.88 %
Rwork0.2021 --
obs0.2035 43517 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→33.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 334 0 220 2499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062373
X-RAY DIFFRACTIONf_angle_d0.9153303
X-RAY DIFFRACTIONf_dihedral_angle_d10.3851330
X-RAY DIFFRACTIONf_chiral_restr0.054359
X-RAY DIFFRACTIONf_plane_restr0.007367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.72930.34261550.2752683X-RAY DIFFRACTION100
1.7293-1.77260.27751380.24652715X-RAY DIFFRACTION100
1.7726-1.82050.2691400.23232731X-RAY DIFFRACTION100
1.8205-1.87410.28211460.22552707X-RAY DIFFRACTION100
1.8741-1.93450.2251270.22042734X-RAY DIFFRACTION100
1.9345-2.00370.26381340.20822741X-RAY DIFFRACTION100
2.0037-2.08390.24431270.21152750X-RAY DIFFRACTION100
2.0839-2.17870.20231460.20512728X-RAY DIFFRACTION100
2.1787-2.29360.24451460.19982742X-RAY DIFFRACTION100
2.2936-2.43720.2191320.20842770X-RAY DIFFRACTION100
2.4372-2.62530.22971340.21042797X-RAY DIFFRACTION100
2.6253-2.88940.23931520.21382754X-RAY DIFFRACTION100
2.8894-3.30720.21221300.20532804X-RAY DIFFRACTION100
3.3072-4.16550.22721620.18722812X-RAY DIFFRACTION100
4.1655-33.86350.20971560.18142924X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00970.04690.01110.16280.10640.170.0902-0.1719-0.10110.05410.01-0.0499-0.03130.0670.01310.1514-0.0018-0.06630.22310.02870.206710.0738172.08090.224
20.02940.03510.05430.1301-0.01110.05480.0391-0.04760.0050.04630.03060.01950.04740.12260.12350.18390.0087-0.01840.34980.05550.1102-0.2026173.177521.5111
30.0155-0.0179-0.01980.0142-0.00380.06360.0503-0.183-0.06560.10020.01910.0527-0.03310.0669-00.1783-0.0213-0.01150.22860.05020.194-5.9461173.562513.6338
40.08740.0998-0.00240.099-0.04620.18550.0585-0.0667-0.0610.0072-0.0022-0.00690.11760.08730.00050.22290.0325-0.02690.1529-0.00720.18923.526163.9284-4.1199
50.0246-0.0170.01960.021-0.0180.01570.0042-0.2886-0.13290.0575-0.07560.0381-0.01280.09470.00010.1822-0.00080.00260.24980.04060.1514-2.0445175.826612.4165
60.10250.10890.01030.1569-0.01490.0776-0.02510.1237-0.2727-0.09850.0035-0.02190.19080.2136-0.02910.24960.10760.0020.2039-0.03470.24313.3475159.2037-7.4913
70.03390.02650.04530.03310.02440.069-0.16310.0256-0.3198-0.0941-0.18220.02720.08370.0122-0.02410.4671-0.27970.10420.45340.04210.6562-18.6573155.867812.8832
80.11380.0561-0.04670.036-0.02130.0119-0.0067-0.1103-0.05560.0756-0.1575-0.09370.1455-0.1898-0.07440.2932-0.3093-0.0560.25640.13071.0254-17.4831154.368416.4276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 168 )
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 278 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 8 )
8X-RAY DIFFRACTION8chain 'G' and (resid 9 through 16 )

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