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- PDB-5vu8: TNA polymerase, closed ternary complex -

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Basic information

Entry
Database: PDB / ID: 5vu8
TitleTNA polymerase, closed 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


DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA 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-9O7 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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)99,2217
Polymers98,6713
Non-polymers5504
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-49 kcal/mol
Surface area37850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.288, 107.360, 147.732
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, 5 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.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M sodium sulfate, 0.1 M MES, pH 4.0, 3% w/v 1,6-hexanediol, 19% PEG3350

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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: Oct 2, 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: 3.2→43.424 Å / Num. obs: 19544 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 9.7
Reflection shellResolution: 3.2→3.29 Å / Rmerge(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.2→43.424 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.98
RfactorNum. reflection% reflection
Rfree0.2946 1616 8.27 %
Rwork0.2577 --
obs0.2608 19544 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→43.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 528 32 1 6681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026880
X-RAY DIFFRACTIONf_angle_d0.549410
X-RAY DIFFRACTIONf_dihedral_angle_d13.3214056
X-RAY DIFFRACTIONf_chiral_restr0.0391019
X-RAY DIFFRACTIONf_plane_restr0.0031108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29410.38551340.36561472X-RAY DIFFRACTION100
3.2941-3.40040.36721310.34421456X-RAY DIFFRACTION100
3.4004-3.52190.32671300.33241465X-RAY DIFFRACTION99
3.5219-3.66290.37831340.32881468X-RAY DIFFRACTION99
3.6629-3.82950.30671350.29661488X-RAY DIFFRACTION100
3.8295-4.03120.38421320.29861474X-RAY DIFFRACTION100
4.0312-4.28360.26391340.23331476X-RAY DIFFRACTION99
4.2836-4.6140.26341330.21341472X-RAY DIFFRACTION100
4.614-5.07770.27251340.19991496X-RAY DIFFRACTION100
5.0777-5.81090.26921360.23191508X-RAY DIFFRACTION100
5.8109-7.31550.27751380.28081542X-RAY DIFFRACTION100
7.3155-43.42830.27341450.22921611X-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)
13.3297-1.67760.59632.0447-0.06370.8314-0.0172-0.0090.12080.1733-0.0579-0.13050.0815-0.039200.8711-0.07650.00270.7755-0.04140.8494101.3459143.6048483.5694
20.4117-0.22560.09151.40230.73271.19040.06480.06750.0874-0.1769-0.09140.10760.0951-0.191-00.8089-0.03860.05580.86870.05960.861488.9518126.4301468.5344
30.829-0.8331-0.63621.2130.01681.40390.11610.44720.4819-0.37070.18220.4877-0.577-0.56620.00011.6120.2254-0.04511.2490.11281.210678.2455137.4132443.3424
40.5321-0.36090.19430.231-0.12380.0626-0.33270.62530.9054-0.858-0.0309-0.4669-0.71540.6-0.00031.6975-0.0571-0.0621.16810.26961.243595.3501131.133445.1907
50.00960.0366-0.00320.0605-0.0038-0.00420.40380.34570.0619-0.11850.0069-0.33860.18820.15870.00022.08440.0067-0.1041.48940.11140.964993.9169131.3241441.4398
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 758 )
4X-RAY DIFFRACTION4chain 'T' and (resid 3 through 16 )
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 11 )

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