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- PDB-9oay: TNA polymerase, 8-64, ternary complex -

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Basic information

Entry
Database: PDB / ID: 9oay
TitleTNA polymerase, 8-64, ternary complex
Components
  • 8-64, TNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / Enzyme Engineering / B-Family Polymerase / TNA Polymerase / Polymerase / Ternary Complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homologyChem-9O7 / IODIDE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLee, J.J. / Maola, V.A. / Chim, N. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1946312 United States
CitationJournal: To Be Published
Title: Directed Evolution of a TNA Polymerase Identifies Independent Paths to Fidelity and Catalysis
Authors: Maola, V.A. / Lee, J.J. / Holguin, M.J. / Quijano, R.N. / Nguyen, K.K. / Ho, K.L. / Medina, J.V. / Botello-Cornejo, E. / Barpuzary, B. / Chim, N. / Chaput, J.C.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-64, TNA polymerase
T: Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7787
Polymers97,1143
Non-polymers6644
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.713, 101.530, 110.675
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 8-64, TNA polymerase


Mass: 87041.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Homologous Recombination from Thermococcus gorgonarius (Tgo), Pyrococcus Deep Vent (DV), Thermococcus 9N (9N), and Thermococcus kodakarensis (Kod)
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain Template


Mass: 6439.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer


Mass: 3633.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 72 molecules

#4: Chemical ChemComp-9O7 / [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate


Mass: 477.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium iodide, 20 % polyethylene glycol 3350, and 0.1 M taurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→48.59 Å / Num. obs: 38977 / % possible obs: 99.87 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0734 / Net I/σ(I): 19.45
Reflection shellResolution: 2.38→2.47 Å / Rmerge(I) obs: 0.7658 / Num. unique obs: 3519 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→48.59 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1994 5.58 %
Rwork0.2162 33761 -
obs0.219 35755 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.48 Å2
Refinement stepCycle: LAST / Resolution: 2.38→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 633 32 68 6875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287019
X-RAY DIFFRACTIONf_angle_d0.5229612
X-RAY DIFFRACTIONf_chiral_restr0.03981031
X-RAY DIFFRACTIONf_plane_restr0.00381121
X-RAY DIFFRACTIONf_dihedral_angle_d18.85411152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.34471460.26192339X-RAY DIFFRACTION99.8
2.44-2.510.3121330.26282419X-RAY DIFFRACTION99.84
2.51-2.580.32041470.26832355X-RAY DIFFRACTION99.96
2.58-2.660.31571300.26262387X-RAY DIFFRACTION99.84
2.66-2.760.33641390.27152383X-RAY DIFFRACTION99.92
2.76-2.870.30341440.24252379X-RAY DIFFRACTION99.96
2.87-30.27781440.23452396X-RAY DIFFRACTION99.92
3-3.160.30991430.22322382X-RAY DIFFRACTION100
3.16-3.350.27191390.23312415X-RAY DIFFRACTION99.92
3.35-3.610.27421490.21842392X-RAY DIFFRACTION99.92
3.61-3.980.26351280.20722440X-RAY DIFFRACTION99.73
3.98-4.550.25291540.1872434X-RAY DIFFRACTION99.96
4.55-5.730.22471400.19652455X-RAY DIFFRACTION99.92
5.73-48.590.22921580.20192585X-RAY DIFFRACTION99.78
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)
11.697704084860.1618043921260.04830926880121.68620975790.5343618176051.965474279920.0915912933241-0.0816648018919-0.0783139219293-0.0300897900509-0.1158735043010.0381429328820.245372246055-0.505914847079-7.89702926982E-50.361175306095-0.0664408990168-0.005624184456650.5164066368090.03339721785840.337327655236-24.9162989991-5.3821090836824.4212514105
22.506995151141.22039962260.4052295643882.571699082430.6169358406241.692542016960.319002300866-0.455052495381-0.1363316811810.500426714417-0.228967751479-0.1539162647440.3082146143490.0197416777879-6.19157424437E-50.626689888887-0.007868772399340.02816866830690.48343578363-0.01928098976770.449037306474-2.9439796048814.57342384343.9332623149
31.055604005310.85958869695-0.09911426627671.431083611110.7940605755991.020888605620.08410340888080.1141249462350.1779864875180.2302594133760.0943741555551-0.1650393491430.03811908227460.374963238091-3.41203274964E-50.5190812204280.0687141503128-0.0330360831960.452788850666-0.01803893461640.4715931876362.1924001319715.71283942730.2803495507
41.575807657070.560106601956-0.5460655738180.7856500028090.02896224266971.11008429698-0.09978410609920.08171079027330.130582834936-0.08782364844470.0688857446068-0.147335115092-0.3390088809610.05460451766648.77277089738E-50.468184498646-0.00700762946987-0.03670346662280.3511923430480.03329083916530.470087643237.9476116386710.99863589222.55420945108
51.3298230036-0.4068275666690.4947070607061.770869468770.2530856500640.998174931604-0.0306539157421-0.943994212033-0.6408012714190.5103716298790.0407677213667-0.457183838309-0.2642516527970.306334252610.001152977185620.529323671270.0520474708953-0.04449776952210.8184020309630.131776796840.70934671947326.35764900693.8763908441527.9066031099
60.07775475707490.07220931610870.05428568991180.0679149581640.05636309596660.05918071991040.193992735539-0.4467970762750.489121424448-0.3266710513-0.576900817982-1.570010682640.6763984901750.487959562179-0.000316462927720.8593331575130.1456656634780.1104246216641.170465830970.1393320046620.975225803085-7.21667125376-3.3719112335526.1461176492
70.4839252848340.5312364507650.1788747254090.6332730425380.379312398840.682029196256-0.3604549111730.00910185955551-0.5421394550760.4829541956350.244709969041-0.470173272030.1856770788310.2870219452380.0007454521710650.4799717120440.168353292358-0.06776593387190.5558373148580.006298474781640.77802238075920.524009609-4.4786472363413.863821097
80.05778555300240.06964421702970.1293014612910.1695470439170.171242694230.284319198011-0.08921783405130.457352072535-0.892081017221-0.0511229598701-0.4230377493570.04380932249130.2845356112820.982072700583-0.008814887776140.5119863428150.2273579682070.02220874029820.8885833883270.1641930733091.0396944162123.0485319093-5.0505322182614.2373546473
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 123 )AA1 - 1231 - 123
22chain 'A' and (resid 124 through 255 )AA124 - 255124 - 255
33chain 'A' and (resid 256 through 364 )AA256 - 364256 - 364
44chain 'A' and (resid 365 through 652 )AA365 - 652365 - 652
55chain 'A' and (resid 653 through 750 )AA653 - 750653 - 750
66chain 'T' and (resid 4 through 8 )TB4 - 8
77chain 'T' and (resid 9 through 21 )TB9 - 21
88chain 'P' and (resid 1 through 11 )PC1 - 11

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