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- PDB-9oau: TNA polymerase, 7-47, binary complex -

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Basic information

Entry
Database: PDB / ID: 9oau
TitleTNA polymerase, 7-47, binary complex
Components
  • 7-47, TNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / Enzyme Engineering / B-Family Polymerase / TNA Polymerase / Polymerase / Binary Complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homologyChem-5CY / DNA / DNA (> 10)
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: Nat Commun / Year: 2025
Title: Directed evolution of a TNA polymerase identifies independent paths to fidelity and catalysis.
Authors: Hajjar, M. / 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
Revision 1.1Dec 31, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-47, TNA polymerase
T: Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1349
Polymers99,4733
Non-polymers6616
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-50 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.216, 110.570, 124.260
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 7-47, TNA polymerase


Mass: 89999.211 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: 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)

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Non-polymers , 4 types, 446 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-5CY / 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium / N,N'-(dipropyl)-tetramethylindodicarbocyanine


Mass: 471.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N2O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
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, 19 % glycerol, and 9 % polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50.6 Å / Num. obs: 62311 / % possible obs: 98.23 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.94
Reflection shellResolution: 2.18→2.258 Å / Rmerge(I) obs: 0.265 / Num. unique obs: 6183 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
iMOSFLMdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→50.6 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 2000 3.21 %
Rwork0.1884 60311 -
obs0.1896 62311 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.13 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 635 45 440 7358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287131
X-RAY DIFFRACTIONf_angle_d1.00129753
X-RAY DIFFRACTIONf_chiral_restr0.04071039
X-RAY DIFFRACTIONf_plane_restr0.00381141
X-RAY DIFFRACTIONf_dihedral_angle_d16.581167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.26271440.21694318X-RAY DIFFRACTION99.44
2.23-2.290.27771410.21214284X-RAY DIFFRACTION99.39
2.29-2.360.24841420.20424274X-RAY DIFFRACTION99.1
2.36-2.440.23251430.2014309X-RAY DIFFRACTION99.02
2.44-2.520.23681420.20244289X-RAY DIFFRACTION98.99
2.52-2.630.25771390.20474191X-RAY DIFFRACTION96.5
2.63-2.750.27931390.21394193X-RAY DIFFRACTION96.4
2.75-2.890.23281440.2074336X-RAY DIFFRACTION99.36
2.89-3.070.28411430.2054343X-RAY DIFFRACTION99.31
3.07-3.310.23241440.20734320X-RAY DIFFRACTION98.85
3.31-3.640.20951440.18534333X-RAY DIFFRACTION98.48
3.64-4.170.19921400.16454247X-RAY DIFFRACTION95.85
4.17-5.250.18241460.14894417X-RAY DIFFRACTION98.94
5.25-50.60.20121490.17984457X-RAY DIFFRACTION95.92
Refinement TLS params.Method: refined / Origin x: -32.0006138588 Å / Origin y: -2.27749395702 Å / Origin z: 13.2230858692 Å
111213212223313233
T0.159661282711 Å20.00209233661452 Å20.0133934633412 Å2-0.187226404545 Å20.00345844135644 Å2--0.188473973512 Å2
L0.0486409714881 °2-0.0397802213992 °20.0530228267597 °2-0.265202517 °20.0313015016078 °2--0.320773951231 °2
S0.00114317359546 Å °-0.00203563705493 Å °-0.0214056847098 Å °0.0157321788506 Å °-0.00692541988611 Å °-0.00747213176127 Å °0.0273785734869 Å °0.0490229942556 Å °7.01297750633E-5 Å °
Refinement TLS groupSelection details: all

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