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- PDB-5vu7: TNA polymerase, open ternary complex -

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Basic information

Entry
Database: PDB / ID: 5vu7
TitleTNA polymerase, open ternary complex
Components
  • DNA polymerase
  • DNA template
  • DNA/TNA hybrid primer
KeywordsTRANSFERASE/DNA / protein-nucleic acid complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb 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 Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb 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-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FA2 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.72 Å
AuthorsChim, N. / Chaput, J.C.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for TNA synthesis by an engineered TNA polymerase.
Authors: Chim, N. / Shi, C. / Sau, S.P. / Nikoomanzar, A. / Chaput, J.C.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA template
P: DNA/TNA hybrid primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1096
Polymers98,6713
Non-polymers4383
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-44 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.550, 112.610, 145.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase / Kod-RI


Mass: 90130.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA template


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA/TNA hybrid primer


Mass: 3642.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FA2 / 5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE


Type: RNA linking / Mass: 317.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N5O6P

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M sodium sulfate, 0.1 M MES, pH 5.5, 3% w/v 1,6-hexanediol, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 18, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→49.1 Å / Num. obs: 29340 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.0738 / Net I/σ(I): 7.6
Reflection shellResolution: 2.72→2.79 Å / Rmerge(I) obs: 0.575

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.72→49.098 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.76
RfactorNum. reflection% reflection
Rfree0.2677 1998 6.81 %
Rwork0.2144 --
obs0.218 29340 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.72→49.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 506 26 0 6746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036947
X-RAY DIFFRACTIONf_angle_d0.6249478
X-RAY DIFFRACTIONf_dihedral_angle_d20.2164111
X-RAY DIFFRACTIONf_chiral_restr0.0431017
X-RAY DIFFRACTIONf_plane_restr0.0041123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7201-2.78810.36851420.33041946X-RAY DIFFRACTION98
2.7881-2.86350.38731410.30791923X-RAY DIFFRACTION98
2.8635-2.94770.37551420.29221940X-RAY DIFFRACTION98
2.9477-3.04290.3081420.27651937X-RAY DIFFRACTION98
3.0429-3.15160.33111420.28361931X-RAY DIFFRACTION98
3.1516-3.27780.37031410.2791931X-RAY DIFFRACTION98
3.2778-3.42690.30311400.24241939X-RAY DIFFRACTION97
3.4269-3.60750.29581410.2241928X-RAY DIFFRACTION98
3.6075-3.83350.2711440.20831960X-RAY DIFFRACTION98
3.8335-4.12930.24551420.19031950X-RAY DIFFRACTION97
4.1293-4.54460.22261430.16841957X-RAY DIFFRACTION97
4.5446-5.20160.21221430.16281960X-RAY DIFFRACTION97
5.2016-6.5510.21391460.18921994X-RAY DIFFRACTION97
6.551-49.10560.21731490.17812046X-RAY DIFFRACTION95
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)
12.5415-1.43130.73912.1353-0.08650.84220.01770.02090.10490.14070.0114-0.49290.02240.2119-0.00010.3328-0.035-0.04230.3336-0.01280.426234.745834.9082328.5966
21.8289-0.48980.49383.1768-0.82922.05360.02570.18040.0598-0.05110.0469-0.05010.01030.096300.2522-0.0270.02240.3360.02150.29159.393750.1824317.5625
30.38690.02250.09591.3264-0.2540.6197-0.04710.0041-0.0559-0.09610.0844-0.0190.2348-0.044-0.00020.368-0.0207-0.07570.38310.00250.371718.055216.0635317.5585
40.4586-0.1507-0.2363.6751-1.22571.86-0.02080.07030.0069-0.83840.29720.68770.391-0.23730.02010.6294-0.0984-0.24870.46780.07120.50291.916922.1577295.2364
50.6248-0.6361-0.09480.8045-0.22970.57650.30560.31330.0573-0.6323-0.1939-0.59150.02970.11-0.00340.8614-0.0175-0.04830.60230.00940.379618.019922.6562293.4303
60.34690.2596-0.03060.2119-0.01570.00370.19630.45170.1525-0.96530.1274-0.25431.44610.71620.01291.11420.0855-0.04830.85160.01270.498517.640722.8727287.8117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 156 )
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 532 )
4X-RAY DIFFRACTION4chain 'A' and (resid 533 through 756 )
5X-RAY DIFFRACTION5chain 'T' and (resid 3 through 15 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 11 )

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