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- PDB-5vu5: TNA polymerase, apo -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5vu5
TitleTNA polymerase, apo
ComponentsDNA polymerase
KeywordsTRANSFERASE / protein-nucleic acid 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
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Oct 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


Theoretical massNumber of molelcules
Total (without water)90,1311
Polymers90,1311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area36230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.819, 110.620, 111.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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

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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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6.0, 20% PEG3000

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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 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: 2.8→55.31 Å / Num. obs: 19774 / % possible obs: 86.4 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.319 / Net I/σ(I): 7.4
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.157

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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 1WNS

1wns


Resolution: 2.8→55.31 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.317 1433 7.25 %
Rwork0.2677 --
obs0.2711 19774 86.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 0 0 5738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025867
X-RAY DIFFRACTIONf_angle_d0.5597918
X-RAY DIFFRACTIONf_dihedral_angle_d14.5473561
X-RAY DIFFRACTIONf_chiral_restr0.042852
X-RAY DIFFRACTIONf_plane_restr0.0041014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.44571340.42591737X-RAY DIFFRACTION83
2.9001-3.01620.4351360.40011749X-RAY DIFFRACTION84
3.0162-3.15350.38331390.36731760X-RAY DIFFRACTION84
3.1535-3.31970.37471420.3651760X-RAY DIFFRACTION85
3.3197-3.52770.3641330.31051795X-RAY DIFFRACTION86
3.5277-3.80.33091410.28491830X-RAY DIFFRACTION87
3.8-4.18230.28731450.26091861X-RAY DIFFRACTION88
4.1823-4.78720.25511500.23251885X-RAY DIFFRACTION88
4.7872-6.03020.28981510.24751948X-RAY DIFFRACTION90
6.0302-55.32080.31561620.22072016X-RAY DIFFRACTION89
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)
13.17422.57141.23823.4677-0.21334.6453-0.51250.4360.2225-0.15680.4268-0.1003-0.72260.2078-0.00220.47870.01310.09680.46450.00760.409317.96131.8695-10.2571
22.25290.4826-1.73394.28410.22634.5863-0.44070.6363-0.2298-1.43890.4816-0.57290.6735-0.1685-0.07420.8839-0.17820.04890.7665-0.07410.52299.1341-24.3184-25.8043
31.43110.69730.6652.04140.21982.96110.1509-0.3287-0.34320.4354-0.0519-0.0690.3392-0.2245-0.09440.59150.01260.00290.62760.06290.438113.133-17.69468.1239
41.4790.29090.10342.93071.07965.90880.37920.0935-0.97780.0639-0.152-0.31220.44270.2165-0.23130.6379-0.1428-0.25180.8203-0.11911.372612.4754-49.55547.4049
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 758 )

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