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- PDB-5vu6: TNA polymerase binary complex with primer/template duplex -

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Basic information

Entry
Database: PDB / ID: 5vu6
TitleTNA polymerase binary complex with primer/template duplex
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
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)98,6873
Polymers98,6873
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-23 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.090, 110.800, 149.080
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: 3658.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, pH 6.0, 16% PEG3500, 0.2 M sodium sulfate, Silver Bullet Bio Additive #56

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 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→88.93 Å / Num. obs: 22536 / % possible obs: 99.71 % / Redundancy: 12 % / Rmerge(I) obs: 0.0912 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.12 Å / Rmerge(I) obs: 0.779

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K8Z

4k8z


Resolution: 3→88.928 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 1304 5.79 %
Rwork0.2355 --
obs0.2382 22536 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→88.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 529 0 0 6743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056942
X-RAY DIFFRACTIONf_angle_d0.7489480
X-RAY DIFFRACTIONf_dihedral_angle_d20.0274110
X-RAY DIFFRACTIONf_chiral_restr0.0451021
X-RAY DIFFRACTIONf_plane_restr0.0051124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.12020.36581380.32522258X-RAY DIFFRACTION99
3.1202-3.26220.32821430.3062338X-RAY DIFFRACTION99
3.2622-3.43420.3151410.27942296X-RAY DIFFRACTION100
3.4342-3.64940.3251430.25052344X-RAY DIFFRACTION100
3.6494-3.93110.30641460.23532359X-RAY DIFFRACTION100
3.9311-4.32670.29511440.22312334X-RAY DIFFRACTION100
4.3267-4.95280.27591460.20412374X-RAY DIFFRACTION100
4.9528-6.23970.25141480.2292401X-RAY DIFFRACTION100
6.2397-88.96740.231550.2132528X-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)
12.83-1.1552-0.77242.3939-0.43651.37910.09140.2181-0.04720.13920.20380.6819-0.0339-0.35120.00050.5165-0.00670.00350.57730.0760.6511-1.484320.4796187.4952
22.027-0.6627-0.46211.94860.12871.77370.1430.2538-0.0703-0.2053-0.04810.07920.27240.010200.54450.05350.00530.5394-0.03160.537123.87574.8904176.8326
30.39620.2196-0.02551.8406-0.45630.61940.030.00450.0972-0.02470.0385-0.0133-0.19660.0647-00.50680.01860.04150.5298-0.03670.477515.31639.1487176.2509
41.50210.161-0.22552.1540.64941.8081-0.00110.1862-0.2114-0.08450.0587-0.30360.10810.19710.00020.62250.0259-0.00580.6269-0.00860.535532.094833.2714154.3415
50.7698-0.2754-0.20250.21040.06740.1970.15020.6156-0.19020.08550.06040.30740.2776-0.3046-0.00020.87580.0721-0.04460.739-0.09420.632615.434732.5278150.603
60.38710.15280.15370.0510.05760.0573-0.14050.93970.4442-1.14440.19040.2571-1.08280.16420.00061.1474-0.0561-0.12321.0222-0.05920.716716.860232.4364146.6123
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 16 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 11 )

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