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- PDB-6wyb: RTX (Reverse Transcription Xenopolymerase) in complex with an RNA... -

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Basic information

Entry
Database: PDB / ID: 6wyb
TitleRTX (Reverse Transcription Xenopolymerase) in complex with an RNA/DNA hybrid
Components
  • DNA polymerase
  • DNA strandDNA
  • RNA strand
KeywordsTRANSFERASE/RNA/DNA / Reverse transcription / proofreading / 3' to 5' exonuclease / Thumb / RTX / KOD / Reverse Tanscription Xenopolymerase / REPLICATION / RNA / DNA / TRANSFERASE-RNA-DNA complex
Function / homology
Function and homology information


DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B ...DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
3,3',3''-phosphanetriyltripropanoic acid / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
Thermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChoi, W.S. / He, P. / Pothukuchy, A. / Gollihar, J. / Ellington, A.D. / Yang, W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: How a B family DNA polymerase has been evolved to copy RNA.
Authors: Choi, W.S. / He, P. / Pothukuchy, A. / Gollihar, J. / Ellington, A.D. / Yang, W.
#1: Journal: Science / Year: 2016
Title: Synthetic evolutionary origin of a proofreading reverse transcriptase.
Authors: Ellefson, J.W. / Gollihar, J. / Shroff, R. / Shivram, H. / Iyer, V.R. / Ellington, A.D.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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: DNA polymerase
B: RNA strand
C: DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6979
Polymers99,1023
Non-polymers5956
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-30 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 112.940, 148.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABC

#1: Protein DNA polymerase /


Mass: 90023.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0VWU9, DNA-directed DNA polymerase
#2: RNA chain RNA strand


Mass: 5105.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermococcus kodakarensis KOD1 (archaea)
#3: DNA chain DNA strand / DNA


Mass: 3973.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermococcus kodakarensis KOD1 (archaea)

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Non-polymers , 4 types, 149 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 2 M ammonium sulfate, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 11, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 40901 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.88
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2997 / CC1/2: 0.658 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K8Z

4k8z


Resolution: 2.5→29.97 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 32.1924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 1000 2.45 %
Rwork0.267 39815 -
obs0.2674 40815 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5855 477 37 143 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876560
X-RAY DIFFRACTIONf_angle_d1.14128977
X-RAY DIFFRACTIONf_chiral_restr0.23911005
X-RAY DIFFRACTIONf_plane_restr0.00671065
X-RAY DIFFRACTIONf_dihedral_angle_d28.39232483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.38641410.35325613X-RAY DIFFRACTION99.88
2.63-2.80.35621400.30845604X-RAY DIFFRACTION99.93
2.8-3.010.30811420.30345659X-RAY DIFFRACTION99.9
3.01-3.320.28011420.29235640X-RAY DIFFRACTION99.93
3.32-3.790.29031420.27035668X-RAY DIFFRACTION99.76
3.79-4.780.26351440.23895699X-RAY DIFFRACTION99.61
4.78-29.970.2651490.25195932X-RAY DIFFRACTION99.22
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)
15.17001860748-1.073935966180.5345394296034.19114235029-0.9105662568861.335142923240.1890024707590.2181682687340.869617173813-0.190456901418-0.1350673050940.502144155205-0.0566587281070.153570694775-4.21334811134E-120.476029384229-0.0867688362980.06058382827580.466875831767-0.1433140750090.50962644613621.605975373541.906905109334.18163074
20.9688878383780.4243449890660.6305564926454.02969401850.5492923481712.08872404834-0.01698720908160.191236617654-0.0416415166849-0.5719602385780.2659716100440.01893417243440.3682910400580.463764564648-4.83095236552E-100.6070638199040.0934318873642-0.08651511298920.554918159003-0.09615890024380.37338160832323.172459561413.139690615226.9911281461
31.50872117423-0.7214483842510.308049793980.4058141211111.210144357252.157418869750.3066047673250.162398747586-0.214769041267-0.3106646649340.04813698410230.8040633701330.0223440879145-0.909039936658-6.20756795151E-91.010406244470.0160959241916-0.3126077283340.879036521080.05539221026790.8164324995861.3462768210310.81902634398.08662779941
40.348783234624-0.129037455015-0.2360039798650.0719358933075-0.5422023069470.7906211265260.6720964479580.5999339919240.2485155753790.425816227599-0.102115965548-0.708723516461-0.977142109780.3261713863653.28223208076E-92.333999807380.209808830099-0.001873141744711.27399126387-0.07866347618041.146870905069.8087100489735.428951622-6.21919578086
50.06867012440510.233839897031-0.1261384063180.05947012197370.0265857115594-0.006442913338760.349964812614-1.126105021060.07575051771950.09110752448380.715379407818-0.077182946858-0.08344780106060.10734759929-6.79936979576E-72.139078007920.09160418056290.1964212073171.8597862090.1007968012961.0191813760321.486006070724.6345158145-4.7880406882
60.121829447152-0.0183498157253-0.0683850040055-0.089609066524-0.0699901885553-0.04407494892880.429156194062-0.17726278581-0.282175350931-0.5495105303380.737143251828-0.108236910726-0.2424936307620.9880566797121.36036286455E-72.15049369286-0.07789026858110.224694215951.57434956112-0.05132730979240.97716559421120.768777230424.2258750077-2.11442414238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 337 )
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 530 )
3X-RAY DIFFRACTION3chain 'A' and (resid 531 through 651 )
4X-RAY DIFFRACTION4chain 'A' and (resid 652 through 756 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 16 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 12 )

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