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- PDB-6wya: RTX (Reverse Transcription Xenopolymerase) in complex with a DNA ... -

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Basic information

Entry
Database: PDB / ID: 6wya
TitleRTX (Reverse Transcription Xenopolymerase) in complex with a DNA duplex and dAMPNPP
Components
  • DNA polymerase
  • DNA strand 1DNA
  • DNA strand 2DNA
KeywordsTRANSFERASE/DNA / Reverse transcription / proofreading / 3' to 5' exonuclease / Thumb / RTX / KOD / Reverse Tanscription Xenopolymerase / REPLICATION / RNA / DNA / TRANSFERASE-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
ACETATE ION / Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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: DNA strand 1
C: DNA strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,13013
Polymers103,2133
Non-polymers91710
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-61 kcal/mol
Surface area38990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.960, 96.360, 112.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA strand 1 / DNA


Mass: 7033.574 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
#3: DNA chain DNA strand 2 / DNA


Mass: 6155.975 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)

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Non-polymers , 6 types, 273 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium acetate, 20% PEG3350

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2017
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: 2.41→50 Å / Num. obs: 39853 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 50.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.02
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2913 / CC1/2: 0.714 / % possible all: 100

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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: 2.41→42.78 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 1002 2.52 %
Rwork0.1659 38819 -
obs0.1672 39821 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.84 Å2
Refinement stepCycle: LAST / Resolution: 2.41→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6207 855 55 263 7380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877422
X-RAY DIFFRACTIONf_angle_d1.01110209
X-RAY DIFFRACTIONf_chiral_restr0.05781101
X-RAY DIFFRACTIONf_plane_restr0.0061156
X-RAY DIFFRACTIONf_dihedral_angle_d27.78122918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.540.29691450.25655449X-RAY DIFFRACTION99.95
2.54-2.70.27291380.23845487X-RAY DIFFRACTION99.95
2.7-2.90.30851430.22125491X-RAY DIFFRACTION100
2.9-3.20.25671400.20185499X-RAY DIFFRACTION99.98
3.2-3.660.25321430.17475535X-RAY DIFFRACTION99.96
3.66-4.610.19311410.13275587X-RAY DIFFRACTION100
4.61-42.780.16311520.13735771X-RAY DIFFRACTION99.81
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)
13.621894412040.875167012484-0.2193917416583.859409554322.80082192016.76970211324-0.0490638898790.0953185539169-0.3575965836610.295257660414-0.1893144303430.2844442119350.655877013244-1.101333190610.2156097853520.332194494873-0.0542233585990.05558982810690.55669166624-0.001716891272590.380391976938-123.436163096188.83710096745.6728778285
24.519639369690.6715776752292.735161199011.387385214291.047797429025.56194522646-0.0322107065524-0.6746126835890.4572616978380.122418367077-0.0372902616926-0.178899286781-0.6512876271080.2003853496090.1191057594520.472659567649-0.1016327912990.1036364225840.545989109069-0.06352878037380.370206398179-98.8455111077206.41577659763.3224861825
33.87464114838-0.01549420348470.4121699134861.68689633113-0.07486070876523.505343955240.133571994701-0.5279460864090.1641944897110.077647147109-0.106091613231-0.304266827821-0.3804923571120.516174399512-0.003881322759070.444516368904-0.1213462324050.02771410702930.469806047774-0.09641443944530.363147319458-92.4323889643204.65289003458.9771339368
42.716122761780.66271251806-1.878393944580.947890928615-0.7830448398042.783361690450.1885869697070.1346551985190.02273595518170.0618378608125-0.0884224817483-0.0406561768752-0.145914272014-0.157360188955-0.05565742956140.2961611761330.0287315170227-0.01813516612190.2879662075450.0128437102980.245687684401-98.4339514717198.12832930624.2873857529
52.15361321832-0.6141937020851.249473352471.32036174087-1.49425167084.74905466444-0.0333009514704-0.1892656919760.07651593024470.115857203931-0.0690825492599-0.206251296791-0.160656415790.2232141526160.1438382704620.340039522193-0.00608100729369-0.01396018654560.289401030407-0.05123011023480.401908096225-71.1436730588198.70108087137.2207580932
69.33887528455-1.87906162141-7.05940916851.161812941651.572770283725.43544418432-0.823751532557-1.52240911825-0.792573496070.914847410446-0.0480081647216-0.4422604254110.5434741098611.549069088630.981893370040.76324463959-0.125802963985-0.01082273608260.5625660852330.0352141010760.600767603386-93.7811480591189.15950277136.2375342312
70.57907798660.823905081259-0.07522707096275.04527775577-2.259752742988.681948175220.2137418446110.319813849995-1.287055326260.601692838702-0.574435335322-0.2948477302040.5883319352650.899228158620.2300341094830.6399445532220.0867616464584-0.02478555075440.5116739538590.06530441822160.993354888263-73.6610057007181.26229433936.125016668
87.80006984557-3.76280938814.951936447543.69246854838-4.799690799116.461497501880.9998915654161.15355274184-1.421799059610.37471425128-0.5878504705140.1429946174450.5964141416732.22728547029-0.2598259155141.412096116330.431831881316-0.3513176321181.126945791640.04992187685781.44763051688-55.8173005399161.07260452545.9279355908
99.1247286845-6.538084191737.130844438514.85861749453-5.541739241426.93860038882-0.0484986110216-0.112841450307-0.5250410778710.6179280679060.5062911208011.31729217145-0.3733277375150.139993788115-0.4291825171641.511580089380.413838112401-0.07648736229791.078711313970.2661940191161.35892725882-58.5351392417162.27721985846.6373615051
109.239835431872.214873939020.8937106400146.61653688523-2.525375316444.255034622450.380597744350.451267352351-1.02283411072-0.53033369679-0.7592201565380.1856183392690.7459830870420.6233629940020.3961867205160.5151439706130.0712437093943-0.00588889871840.553947911316-0.01909223130470.449675147347-78.5662797782185.41152641735.0846992435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 337 )
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 552 )
5X-RAY DIFFRACTION5chain 'A' and (resid 553 through 756 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 5 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 22 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 10 )
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 20 )

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