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- PDB-4xpc: Crystal structure of 5'- CTTATAAATTTATAAG in a host-guest complex -

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Basic information

Entry
Database: PDB / ID: 4xpc
TitleCrystal structure of 5'- CTTATAAATTTATAAG in a host-guest complex
Components
  • DNA (5'-D(*CP*TP*TP*AP*TP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*AP*TP*AP*AP*G)-3')
  • reverse transcriptase
KeywordsTRANSFERASE/DNA / host-guest complex B-DNA non-natural nucleobase pair synthetic biology / 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
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. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain 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 / molecular replacement / Resolution: 1.68 Å
AuthorsGeorgiadis, M.M. / Singh, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111386 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2015
Title: Structural basis for a six nucleotide genetic alphabet.
Authors: Georgiadis, M.M. / Singh, I. / Kellett, W.F. / Hoshika, S. / Benner, S.A. / Richards, N.G.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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*AP*AP*A)-3')
G: DNA (5'-D(P*TP*TP*TP*AP*TP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3846
Polymers34,1983
Non-polymers1863
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.636, 145.273, 46.801
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 / / Pr180gag-pol


Mass: 29347.754 Da / Num. of mol.: 1
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 (E. coli)
References: UniProt: P03355, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: DNA chain DNA (5'-D(*CP*TP*TP*AP*TP*AP*AP*A)-3')


Mass: 2409.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*AP*TP*AP*AP*G)-3')


Mass: 2440.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FULL CRYSTALLIZED SEQUENCE FOR THE DNA CHAINS CORRESPONDS TO THE FOLLOWING SELF-COMPLEMENTARY ...THE FULL CRYSTALLIZED SEQUENCE FOR THE DNA CHAINS CORRESPONDS TO THE FOLLOWING SELF-COMPLEMENTARY 16-MER (DC)(DT)(DT)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DT)(DA)(DT)(DA)(DA)(DG)

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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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.68→29.05 Å / Num. obs: 43118 / % possible obs: 99.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.017 / Net I/σ(I): 24.8 / Num. measured all: 183063 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.68-1.714.40.4313.4954121930.8750.2399.3
9.05-29.053.80.01669.512613290.9990.00996.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→28.692 Å / FOM work R set: 0.8592 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2162 5.02 %
Rwork0.2154 40900 -
obs0.2166 43062 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.329 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 71.27 Å2 / Biso mean: 30.12 Å2 / Biso min: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.0943 Å20 Å20 Å2
2---0.2106 Å20 Å2
3---0.3049 Å2
Refinement stepCycle: final / Resolution: 1.68→28.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 325 12 196 2515
Biso mean--30.35 30 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052408
X-RAY DIFFRACTIONf_angle_d0.9643341
X-RAY DIFFRACTIONf_chiral_restr0.06370
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d19.571915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.71910.291350.25082700283599
1.7191-1.76210.23671420.23642676281899
1.7621-1.80970.22851410.22682662280399
1.8097-1.86290.25441380.22712691282999
1.8629-1.92310.27181460.223826902836100
1.9231-1.99180.2481540.21042696285099
1.9918-2.07150.23281410.20282694283599
2.0715-2.16580.22031460.20427362882100
2.1658-2.27990.23171450.212227002845100
2.2799-2.42270.22351400.211927372877100
2.4227-2.60960.21181350.21182746288199
2.6096-2.8720.24661580.21512729288799
2.872-3.28710.26241320.2212773290599
3.2871-4.13940.20981460.20182739288598
4.1394-28.69660.24241630.20542931309499

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