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- PDB-5vu9: TNA polymerase, translocated product -

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Basic information

Entry
Database: PDB / ID: 5vu9
TitleTNA polymerase, translocated product
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
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 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


Theoretical massNumber of molelcules
Total (without water)98,9863
Polymers98,9863
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-24 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.139, 110.920, 151.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#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
#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: 3957.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium sulfate, 0.1 M MES, pH 5.8, 12% PEG3350, Silver Bullets Bio (Hampton Research) additive #56

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 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: 2.05→45.85 Å / Num. obs: 69934 / % possible obs: 94.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 11
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.789

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.05→45.852 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1809 2.59 %
Rwork0.1903 --
obs0.1914 69936 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→45.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6210 592 0 347 7149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097016
X-RAY DIFFRACTIONf_angle_d0.9279584
X-RAY DIFFRACTIONf_dihedral_angle_d20.3964132
X-RAY DIFFRACTIONf_chiral_restr0.0551029
X-RAY DIFFRACTIONf_plane_restr0.0061127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10540.44631310.36544948X-RAY DIFFRACTION90
2.1054-2.16740.32651320.30694948X-RAY DIFFRACTION91
2.1674-2.23730.27171300.28154950X-RAY DIFFRACTION91
2.2373-2.31730.32851310.26834956X-RAY DIFFRACTION91
2.3173-2.41010.33621340.23085029X-RAY DIFFRACTION92
2.4101-2.51980.26961330.22275022X-RAY DIFFRACTION92
2.5198-2.65260.24661360.21955106X-RAY DIFFRACTION93
2.6526-2.81880.29571420.21265278X-RAY DIFFRACTION96
2.8188-3.03640.26291440.2025437X-RAY DIFFRACTION99
3.0364-3.34180.23261470.1915497X-RAY DIFFRACTION99
3.3418-3.82520.21111460.1665538X-RAY DIFFRACTION99
3.8252-4.81850.17891490.14285585X-RAY DIFFRACTION100
4.8185-45.86380.20891540.17095833X-RAY DIFFRACTION100
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)
11.559-0.7073-0.32380.6559-0.01380.56450.01280.0173-0.13470.13790.0990.16460.0833-0.04320.06230.219-0.02490.04280.26070.04220.325376.0182125.9704188.8131
20.1879-0.0627-0.13711.0316-0.01510.60260.08390.0229-0.0013-0.06780.05260.0652-0.17970.06190.0050.2519-0.02070.05640.2712-0.03420.284288.6246145.094176.752
30.6455-0.26670.13690.91880.50660.83330.09060.0453-0.1032-0.36580.1098-0.18620.12630.18850.08930.55930.02470.12930.3793-0.10110.3586101.0056136.7806151.8141
40.0893-0.0612-0.05280.17770.14010.11060.13490.175-0.0535-0.1910.05410.32320.03610.04770.00070.56030.0301-0.04750.3885-0.01620.327483.7966142.7579154.0735
50.4109-0.2887-0.08220.21140.06810.0290.02240.02980.0407-0.01830.10740.062-0.00430.04310.00290.9910.19-0.15540.95540.01940.523477.0968143.7323129.7901
60.16730.0646-0.09060.0246-0.0350.04920.04430.345-0.0282-0.401-0.0940.1074-0.34390.14850.0130.76590.0904-0.09010.5275-0.06670.296585.1997142.2638145.395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 588 )
3X-RAY DIFFRACTION3chain 'A' and (resid 589 through 757 )
4X-RAY DIFFRACTION4chain 'T' and (resid 1 through 15 )
5X-RAY DIFFRACTION5chain 'T' and (resid 16 through 16 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 11 )

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