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- PDB-8t3x: TNA polymerase, closed ternary -

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Basic information

Entry
Database: PDB / ID: 8t3x
TitleTNA polymerase, closed ternary
Components
  • 10-92, TNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / DNA polymerase / transferase / transferase-DNA complex
Function / homology
Function and homology information


DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-9O7 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsMaola, V. / Chaput, J. / Chim, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nat Catal / Year: 2024
Title: Directed evolution of a highly efficient TNA polymerase achieved by homologous recombination
Authors: Maola, V.A. / Yik, E.J. / Hajjar, M. / Lee, J.J. / Holguin, M.J. / Quijano, R.N. / Nguyen, K.K. / Ho, K.L. / Medina, J.V. / Chim, N. / Chaput, J.C.
History
DepositionJun 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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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)97,4196
Polymers96,6793
Non-polymers7403
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.869, 99.525, 110.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 10-92, TNA polymerase


Mass: 88459.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: engineered from Thermococcus kodakarensis DNA polymerase
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain Template


Mass: 4585.972 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 , 4 types, 50 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Lithium chloride , 0.1 M HEPES pH 6.5, 17.6% PEG 6000

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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 PILATUS3 2M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→45.39 Å / Num. obs: 23008 / % possible obs: 99.03 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.32 Å2 / Rmerge(I) obs: 0.1773 / Net I/σ(I): 11.36
Reflection shellResolution: 2.73→2.828 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 2237 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→45.39 Å / SU ML: 0.4171 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3014 2000 8.7 %
Rwork0.2418 20980 -
obs0.247 22980 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.21 Å2
Refinement stepCycle: LAST / Resolution: 2.73→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 551 45 47 6778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226936
X-RAY DIFFRACTIONf_angle_d0.45199481
X-RAY DIFFRACTIONf_chiral_restr0.03851013
X-RAY DIFFRACTIONf_plane_restr0.00351115
X-RAY DIFFRACTIONf_dihedral_angle_d17.58181120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.42351390.35781456X-RAY DIFFRACTION97.97
2.8-2.870.38761400.33881469X-RAY DIFFRACTION99.02
2.87-2.960.42871400.3221481X-RAY DIFFRACTION99.08
2.96-3.050.35981410.30961478X-RAY DIFFRACTION99.08
3.05-3.160.35961400.31111467X-RAY DIFFRACTION98.65
3.16-3.290.35261410.291477X-RAY DIFFRACTION99.14
3.29-3.440.33191420.27151477X-RAY DIFFRACTION99.02
3.44-3.620.33361410.25561489X-RAY DIFFRACTION98.91
3.62-3.850.31931420.2641494X-RAY DIFFRACTION98.85
3.85-4.140.28741410.22171479X-RAY DIFFRACTION98.78
4.14-4.560.2461460.19431518X-RAY DIFFRACTION99.64
4.56-5.220.24641450.18631534X-RAY DIFFRACTION99.53
5.22-6.570.25691470.21051534X-RAY DIFFRACTION99.7
6.58-45.390.241550.18261627X-RAY DIFFRACTION99.33
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)
10.4371541746420.156343084956-0.03114451901970.2867916607920.0826689502110.619509666430.0326550071946-0.02307281610170.009340440284170.0259734810523-0.00337338712556-0.0514833767190.005390437292580.008362956284791.38804122269E-50.3277404635190.011322988702-0.01720095035290.3349417471430.02311151020330.3703257437171.8598.26620.492
20.0248906941457-0.000465667005010.0478441388818-0.000720849181201-0.005725427541860.102533719098-0.3186786683710.000848465596452-0.0493412884170.2910315231470.206038699354-0.005474080737260.3675485336950.09933557352611.0250924554E-50.4620904937920.0754706841342-0.04971975980340.515342714479-0.06768978591980.46535225998917.229-4.66215.039
30.01247609314780.00619133773301-0.01246702452120.02742408906250.03279137049180.07073444865670.1961429956540.194955159585-0.269897459959-0.236384124533-0.0448455384385-0.08567953953160.12512183990.45716856806-3.91854902046E-50.4446044998370.0835434412877-0.04996725233460.65530587231-0.04819034003690.79987194655319.599-2.56512.663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:748 )A1 - 748
2X-RAY DIFFRACTION2( CHAIN T AND RESID 7:21 )T7 - 21
3X-RAY DIFFRACTION3( CHAIN P AND ( RESID 1:11 OR RESID 12:12 ) ) OR ( CHAIN A AND RESID 801:801 )P1 - 11
4X-RAY DIFFRACTION3( CHAIN P AND ( RESID 1:11 OR RESID 12:12 ) ) OR ( CHAIN A AND RESID 801:801 )P12
5X-RAY DIFFRACTION3( CHAIN P AND ( RESID 1:11 OR RESID 12:12 ) ) OR ( CHAIN A AND RESID 801:801 )A801

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