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- PDB-6isf: Structure of 9N-I DNA polymerase incorporation with dT in the act... -

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Basic information

Entry
Database: PDB / ID: 6isf
TitleStructure of 9N-I DNA polymerase incorporation with dT in the active site
Components
  • DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA polymerase / 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 sp. 9oN-7 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLinwu, S.W. / Maestre-Reyna, M. / Tsai, M.D. / Tu, Y.H. / Chang, W.H.
CitationJournal: Commun Biol / Year: 2019
Title: Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Authors: LinWu, S.W. / Tu, Y.H. / Tsai, T.Y. / Maestre-Reyna, M. / Liu, M.S. / Wu, W.J. / Huang, J.Y. / Chi, H.W. / Chang, W.H. / Chiou, C.F. / Wang, A.H. / Lee, J. / Tsai, M.D.
History
DepositionNov 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: DNA polymerase
B: DNA polymerase
C: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')
D: DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
E: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')
F: DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,38313
Polymers202,1036
Non-polymers2817
Water86548
1
A: DNA polymerase
C: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')
D: DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1325
Polymers101,0513
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-52 kcal/mol
Surface area36600 Å2
MethodPISA
2
B: DNA polymerase
E: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')
F: DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2528
Polymers101,0513
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-81 kcal/mol
Surface area36660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.088, 107.361, 255.665
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 /


Mass: 90939.820 Da / Num. of mol.: 2 / Mutation: D141A, E143A, A485L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. 9oN-7 (archaea) / Strain: 9oN-7 / Gene: pol, polA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q56366, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')


Mass: 4560.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5550.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium Acetate pH4.6, MPD, Glycerol, CaCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→46.38 Å / Num. obs: 62970 / % possible obs: 99.48 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.07432 / Net I/σ(I): 2.93
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.3808 / Num. unique obs: 6160 / CC1/2: 0.632

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSNovember 1, 2016 built 20161205data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8X

4k8x


Resolution: 2.8→46.38 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.882 / SU B: 17.385 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 0.9 / ESU R Free: 0.364 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27162 3128 5 %RANDOM
Rwork0.23165 ---
obs0.23363 59886 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.135 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å2-0 Å20 Å2
2---1.58 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11802 1321 7 54 13184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213569
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711867
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.59518671
X-RAY DIFFRACTIONr_angle_other_deg1.1411.6727347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24651513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.19320.883634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.428151964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9051597
X-RAY DIFFRACTIONr_chiral_restr0.0570.21774
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023079
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0976.4776052
X-RAY DIFFRACTIONr_mcbond_other2.0976.4776051
X-RAY DIFFRACTIONr_mcangle_it3.5739.7177562
X-RAY DIFFRACTIONr_mcangle_other3.5739.7177563
X-RAY DIFFRACTIONr_scbond_it1.8346.1127517
X-RAY DIFFRACTIONr_scbond_other1.8336.1127516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1629.1211109
X-RAY DIFFRACTIONr_long_range_B_refined6.19727888
X-RAY DIFFRACTIONr_long_range_B_other6.19727889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 227 -
Rwork0.356 4317 -
obs--98.4 %

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