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- PDB-9oav: TNA polymerase, 8-64, binary complex -

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Basic information

Entry
Database: PDB / ID: 9oav
TitleTNA polymerase, 8-64, binary complex
Components
  • 8-64, 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: 2.5 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)99,5726
Polymers99,4993
Non-polymers733
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-48 kcal/mol
Surface area35660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.388, 108.034, 123.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 8-64, TNA polymerase


Mass: 90025.250 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.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting 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: 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: 2.5→49.5 Å / Num. obs: 40682 / % possible obs: 99.91 % / Redundancy: 5.2 % / Biso Wilson estimate: 48.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1386 / Net I/σ(I): 8.39
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.8707 / Num. unique obs: 3980 / CC1/2: 0.667

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
PHENIXv1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.5 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1999 4.91 %
Rwork0.2293 --
obs0.2306 40682 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6231 635 3 102 6971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.509
X-RAY DIFFRACTIONf_dihedral_angle_d17.4421154
X-RAY DIFFRACTIONf_chiral_restr0.041038
X-RAY DIFFRACTIONf_plane_restr0.0041139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.38521400.35482712X-RAY DIFFRACTION99
2.56-2.630.35561400.33212705X-RAY DIFFRACTION100
2.63-2.710.32261410.32642737X-RAY DIFFRACTION100
2.71-2.80.34211410.31462724X-RAY DIFFRACTION100
2.8-2.90.35511420.29282741X-RAY DIFFRACTION100
2.9-3.010.30991420.28662735X-RAY DIFFRACTION100
3.01-3.150.26551410.25512739X-RAY DIFFRACTION100
3.15-3.320.26761400.25142732X-RAY DIFFRACTION100
3.32-3.520.29621430.24032750X-RAY DIFFRACTION100
3.52-3.80.2821420.21912767X-RAY DIFFRACTION100
3.8-4.180.21881440.1992777X-RAY DIFFRACTION100
4.18-4.780.20821450.18682790X-RAY DIFFRACTION100
4.78-6.020.22751450.20122829X-RAY DIFFRACTION100
6.02-49.50.20371530.18982945X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -31.5984 Å / Origin y: 2.3135 Å / Origin z: -13.0636 Å
111213212223313233
T0.4831 Å20.0136 Å2-0.0181 Å2-0.5046 Å20.0199 Å2--0.4916 Å2
L0.1282 °20.1056 °2-0.0025 °2-0.39 °20.1185 °2--0.3394 °2
S0.0001 Å °0.0296 Å °0.0362 Å °-0.0139 Å °0.015 Å °-0.0044 Å °-0.0349 Å °0.0439 Å °0 Å °
Refinement TLS groupSelection details: all

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