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- PDB-9oax: TNA polymerase, 5-270, ternary complex -

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Basic information

Entry
Database: PDB / ID: 9oax
TitleTNA polymerase, 5-270, ternary complex
Components
  • 5-270, TNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / Enzyme Engineering / B-Family Polymerase / TNA Polymerase / Polymerase / Binary 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: 3.03 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: 5-270, TNA polymerase
T: Template
P: Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8917
Polymers97,2003
Non-polymers6904
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.441, 101.713, 110.847
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 5-270, TNA polymerase


Mass: 87127.883 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, 9 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 / Feature type: SUBJECT OF INVESTIGATION
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium iodide, 20% PEG 3350, 0.1 M calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.03→48.67 Å / Num. obs: 17539 / % possible obs: 99.61 % / Redundancy: 6.6 % / Biso Wilson estimate: 63.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1628 / Net I/σ(I): 12.57
Reflection shellResolution: 3.03→3.14 Å / Rmerge(I) obs: 1.017 / Num. unique obs: 1729 / CC1/2: 0.769

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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: 3.03→48.67 Å / SU ML: 0.4273 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2777 1751 9.98 %
Rwork0.224 15788 -
obs0.2294 17539 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.16 Å2
Refinement stepCycle: LAST / Resolution: 3.03→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 613 35 5 6783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156988
X-RAY DIFFRACTIONf_angle_d0.38119565
X-RAY DIFFRACTIONf_chiral_restr0.03671026
X-RAY DIFFRACTIONf_plane_restr0.00271118
X-RAY DIFFRACTIONf_dihedral_angle_d18.75631140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.110.37131410.29981177X-RAY DIFFRACTION99.7
3.11-3.20.36561250.27731216X-RAY DIFFRACTION99.78
3.2-3.310.30511320.26671186X-RAY DIFFRACTION99.92
3.31-3.430.38521370.27591188X-RAY DIFFRACTION99.77
3.43-3.560.28741370.24771205X-RAY DIFFRACTION100
3.56-3.720.29891240.22531197X-RAY DIFFRACTION99.85
3.72-3.920.27811450.22311193X-RAY DIFFRACTION99.11
3.92-4.170.25771200.22121206X-RAY DIFFRACTION99.77
4.17-4.490.24751480.20741208X-RAY DIFFRACTION100
4.49-4.940.25521250.18381230X-RAY DIFFRACTION99.85
4.94-5.650.23141350.21121250X-RAY DIFFRACTION99.93
5.65-7.110.28691390.2371239X-RAY DIFFRACTION99.57
7.12-48.670.25611430.19881293X-RAY DIFFRACTION98.29
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)
11.96228747584-1.124034416141.440066939932.05075503902-1.500250650124.092484726410.2042552549110.132813551297-0.108545596718-0.120422662942-0.0905862074944-0.02794810216310.2420906795580.6670318409350.0002855422701140.4534301241790.01001261049820.03753221197780.744476090445-0.1113694030760.52054010167620.6611079321-1.66053555066-27.2099784949
23.44745907037-0.399336394896-0.1635440111141.083850943451.19500159171.563506747430.06583709661060.5859451996650.126509441125-0.326268780896-0.138281653104-0.0659988740777-0.0338586567984-0.2155968665156.52715740061E-50.695800681673-0.03907297051590.02610717213740.6836323245620.05915321576350.5490245186812.8516466816914.798621983-43.8851637089
31.51762929208-0.278519333554-0.7264816425390.9078022794-0.2713676858371.96635752607-0.0845081462673-0.08246392692210.280050882257-0.004832201747940.03910139576730.125509948291-0.2420005730120.01010871352544.15463486348E-50.551481125386-0.0947526835831-0.07307918377630.418664135204-0.05071643451380.5747830187880.0097157692278210.9249766612-15.0568971258
42.2629754602-0.3088117240660.01691280672750.606982012725-0.1856069057191.42709854448-0.1383155219280.216115567698-0.0964304324057-0.06266404603920.0293993907590.267826911929-0.502358215188-0.3434891004611.17139172993E-50.6617308209910.0615167678364-0.008982301338110.4758782433070.001697692631860.682977484513-20.283737424610.3628040524-11.596169933
53.171929297630.663757908723-1.429642749685.99925094716-6.820153800897.88674917835-0.9354589982622.01781074036-0.885902344403-1.39494482843-0.994070891667-1.746149513772.135461466531.15241660662-0.5673462658991.16029012281-0.1853222704710.094548226661.4430361818-0.05742478091461.079426043834.2487054118-1.74878201067-22.4727581542
60.215421707868-0.2292669747910.09695359181360.150075658835-0.228068853480.492201419332-0.197118444387-0.344071151044-0.805255463143-0.4315407317030.0360207826130.3205842693130.252535536376-0.673690443235-9.16937037676E-50.632447635642-0.171607209746-0.01981547483730.774223644954-0.0268772334080.983899893728-22.2121855448-5.03236305294-13.9142159199
70.204686826278-0.2037527213080.1436796882550.477496362617-0.3604120868080.624933614443-0.182977383432-1.15779346919-1.5147632205-0.003220054162780.04655067448610.1935123142770.29164824283-0.724487434746-0.0003528497729460.683758059763-0.0941301339349-0.0108571155741.10084971563-0.1018233457771.36985341112-23.0634269492-4.93724918306-14.1253751123
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 156 )AA1 - 1561 - 156
22chain 'A' and (resid 157 through 266 )AA157 - 266157 - 266
33chain 'A' and (resid 267 through 499 )AA267 - 499267 - 499
44chain 'A' and (resid 500 through 747 )AA500 - 747500 - 747
55chain 'T' and (resid 5 through 9 )TB5 - 9
66chain 'T' and (resid 10 through 21 )TB10 - 21
77chain 'P' and (resid 1 through 11 )PC1 - 11

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