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- PDB-9oaw: TNA polymerase, 10-92, binary complex -

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Basic information

Entry
Database: PDB / ID: 9oaw
TitleTNA polymerase, 10-92, binary complex
Components
  • 10-92, TNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / Enzyme Engineering / B-Family Polymerase / TNA Polymerase / Polymerase / Binary Complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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: 10-92, TNA polymerase
T: Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6307
Polymers99,5323
Non-polymers974
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-54 kcal/mol
Surface area36230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.437, 108.253, 123.775
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

#1: Protein 10-92, TNA polymerase


Mass: 90058.336 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)
#2: DNA chain Template


Mass: 5525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer


Mass: 3948.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 0.1 M imidazole, 0.1 M 2-(N-morpholino) ethanesulfonic acid pH 6, 17.5 % glycerol, and 7.5 % polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→33.3 Å / Num. obs: 61779 / % possible obs: 99.79 % / Redundancy: 6.8 % / Biso Wilson estimate: 51.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1051 / Net I/σ(I): 10.73
Reflection shellResolution: 2.172→2.25 Å / Rmerge(I) obs: 2.163 / Num. unique obs: 6048 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→33.3 Å / SU ML: 0.3066 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 2000 3.24 %
Rwork0.2163 59779 -
obs0.2173 61779 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61 Å2
Refinement stepCycle: LAST / Resolution: 2.17→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6243 635 4 84 6966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217095
X-RAY DIFFRACTIONf_angle_d0.4639702
X-RAY DIFFRACTIONf_chiral_restr0.03921038
X-RAY DIFFRACTIONf_plane_restr0.00391137
X-RAY DIFFRACTIONf_dihedral_angle_d16.76191151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.35091390.31184177X-RAY DIFFRACTION99.01
2.23-2.290.34191420.30554213X-RAY DIFFRACTION99.63
2.29-2.350.31731410.29884224X-RAY DIFFRACTION99.89
2.35-2.430.32571410.29684214X-RAY DIFFRACTION99.93
2.43-2.520.3561420.27614238X-RAY DIFFRACTION99.95
2.52-2.620.34161420.27344234X-RAY DIFFRACTION99.98
2.62-2.740.28791410.2654231X-RAY DIFFRACTION100
2.74-2.880.2981430.25324266X-RAY DIFFRACTION99.98
2.88-3.060.28361410.25954232X-RAY DIFFRACTION99.95
3.06-3.30.25081440.23514294X-RAY DIFFRACTION99.93
3.3-3.630.25181430.22044282X-RAY DIFFRACTION100
3.63-4.150.24831440.19434307X-RAY DIFFRACTION99.93
4.15-5.230.20621460.17434345X-RAY DIFFRACTION99.82
5.23-33.30.19091510.18584522X-RAY DIFFRACTION99.68
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)
12.85501991734-0.03720779872981.029373798050.3651416546070.1015193739361.002092364370.01354899292230.02393937641080.00407260658934-0.01341358656670.007301735674060.0418275617745-0.138169665816-0.0225994556721.85135787723E-50.550142756235-0.002713314173870.04823444715840.411987527497-0.00211424421210.492569315701-39.976811941819.011194014314.2714558336
21.324038370070.007358247313941.543696761571.644696888050.6879043332753.929214683450.1195151001390.0719969906515-0.319609861168-0.01160081400510.122881602370.1014745694080.2394628195370.02820779231999.55311549468E-50.500116748436-0.06397934536650.03139559790130.5233849691910.02551455148830.602136248264-21.5344841710.564277943420.2190876969
30.715490751091-0.508974534652-0.3704085305481.64810892730.9868599206080.988717498462-0.0692368788308-0.007617807097880.0599376095734-0.04488906825970.077007995333-0.0591703830907-0.06482727452760.117845685701-3.57350967691E-50.547755910327-0.021753176815-0.01024843618550.570090367150.01917734996150.513088611674-39.1144305883-4.47843903522-1.09136372627
40.976854265978-0.3621050946830.3930400961660.728197319808-0.3498278462581.45999588143-0.03857096658940.05027062056830.05300969640940.0223830724884-0.0193449490864-0.02431326758870.05952972410330.248586627149-1.34934403513E-50.509164665417-0.003852807906910.03051448781960.5034093795040.003451462905990.543313990458-23.9231209026-19.41086223976.67625005594
52.89662060569-0.00736606145967-0.2329721085170.341937465854-0.6322321355773.33508651655-0.0906449273479-0.3144697115950.1330084401230.4969400257570.103513672804-0.1047619677750.3198872198790.3090389852214.99804788894E-50.624172804727-0.005096416244770.02391026481040.534393193908-0.01019521013690.595496622672-19.8808771093-19.178237792532.3647023989
60.0295752246747-0.0268544218263-0.04335700951360.02365245101140.02909740319460.0424854507794-0.0969262331782-0.5435805583320.290069928730.337661429858-0.330041124813-0.170773266668-0.811684789767-0.8240774876710.0003486088127021.433796722070.1159126537250.1118923587681.25231241403-0.3404038056761.34770104522-43.75617459323.538187569915.7013073623
70.6179500129140.03833297135210.664413817690.3615472052940.3309478255580.890750268710.108754995742-0.31740854797-0.1581125417120.0192685705582-0.1180388568240.4572045153590.321252465233-0.126830821370.000132488221510.712802821524-0.02461201804410.04460092700260.5701643727510.07855886044810.622763582859-36.0673291631-23.44931349223.8217456727
80.2502103532080.1201521565930.04079084187390.5812374871780.5801107224710.6006290305810.0706001119385-0.0777872509347-0.302396786881-1.081516050250.2705695599310.4586813383471.142859198580.2797469360459.0906394723E-51.100232676480.0293941212099-0.0280165593230.8065314622680.1843870322890.915720846247-35.3320662302-24.425723131426.2657147794
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 214 )AA1 - 2141 - 214
22chain 'A' and (resid 215 through 337 )AA215 - 337215 - 337
33chain 'A' and (resid 338 through 499 )AA338 - 499338 - 499
44chain 'A' and (resid 500 through 678 )AA500 - 678500 - 678
55chain 'A' and (resid 679 through 759 )AA679 - 759679 - 759
66chain 'T' and (resid 2 through 6 )TB2 - 6
77chain 'T' and (resid 7 through 19 )TB7 - 19
88chain 'P' and (resid 1 through 11 )PC1 - 11

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