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- PDB-7b0h: TgoT_6G12 Ternary complex -

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Basic information

Entry
Database: PDB / ID: 7b0h
TitleTgoT_6G12 Ternary complex
Components
  • DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')
  • DNA polymerase
KeywordsDNA BINDING PROTEIN / archaea / polymerase
Function / homology
Function and homology information


exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
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 ...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 superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus gorgonarius (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSamson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V. / Herdewijn, P. / Delarue, M.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)G0H7618N Belgium
CitationJournal: Biomolecules / Year: 2020
Title: Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.
Authors: Samson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V.B. / Herdwijn, P. / Delarue, M.
History
DepositionNov 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')
C: DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')
E: DNA polymerase
F: DNA polymerase
G: DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,58914
Polymers191,3566
Non-polymers1,2338
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-62 kcal/mol
Surface area69010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.823, 112.331, 186.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 4 molecules ACDG

#1: DNA chain DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')


Mass: 4009.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')


Mass: 1784.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules EF

#3: Protein DNA polymerase / / TO POL


Mass: 89884.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gorgonarius (archaea) / Gene: pol, polA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56689, DNA-directed DNA polymerase

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Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% PEG 20K and 0.1M MES-NaOH pH 6.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.15→48.92 Å / Num. obs: 33317 / % possible obs: 80.49 % / Redundancy: 2.7 % / Biso Wilson estimate: 112.59 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.89
Reflection shellResolution: 3.15→3.263 Å / Num. unique obs: 1758 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tgo

1tgo


Resolution: 3.15→48.92 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.508
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1648 4.95 %RANDOM
Rwork0.2319 ---
obs0.2327 33317 80.5 %-
Displacement parametersBiso max: 208.98 Å2 / Biso mean: 104.56 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-3.7608 Å20 Å20 Å2
2--1.066 Å20 Å2
3----4.8268 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 3.15→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12134 779 64 0 12977
Biso mean--84.25 --
Num. residues----1513
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4680SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2135HARMONIC5
X-RAY DIFFRACTIONt_it13341HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1682SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8674SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13341HARMONIC20.005
X-RAY DIFFRACTIONt_angle_deg18168HARMONIC20.78
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 3.15→3.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2401 33 4.95 %
Rwork0.2615 634 -
all0.2605 667 -
obs--41.57 %
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)
18.3155-0.09931.18587.58481.03310-0.17060.46590.5442-0.1713-0.0324-0.0949-0.3906-0.14940.2030.3040.0191-0.152-0.20890.152-0.201333.1321-27.305733.5014
28.31551.78631.68618.31550.90831.06420.014-0.09990.54420.54420.5162-0.54420.3770.5309-0.5302-0.19020.1342-0.1520.3040.0214-0.244126.25333.79829.735
34.2361-0.9582-0.37752.11551.60441.3189-0.0971-0.0733-0.06520.10480.2166-0.5442-0.21140.2144-0.11950.1565-0.0358-0.152-0.304-0.12660.199162.4459-18.587646.7455
44.7743-2.38770.36326.90230.99851.09740.08330.14810.5442-0.5442-0.46090.4591-0.2999-0.54420.37770.14870.152-0.0624-0.036-0.152-0.145328.5507-1.133750.9275
52.32040.9871.06714.16150.95420.7231-0.0019-0.3481-0.16620.22510.0728-0.10770.0697-0.3027-0.07090.2426-0.0456-0.1304-0.1520.0933-0.110538.6054-38.134443.9568
61.42422.4717-1.66943.1238-1.16041.37060.1964-0.5442-0.33970.5442-0.13640.54420.0703-0.5442-0.060.025-0.1520.04450.03890.1520.123117.4751-47.769244.7319
70.33360.05530.023.3776-2.339200.01710.0892-0.03790.03450.09120.5442-0.54420.0278-0.1083-0.04930.1520.05850.304-0.14890.1942-0.4128-25.216431.2207
83.0004-0.7531-0.72913.98060.12460.09710.0427-0.07320.54420.0665-0.35320.1807-0.2610.25960.3105-0.304-0.079-0.01260.07440.1520.30434.865434.73391.8715
97.8014-1.027-0.28924.63050.79342.5258-0.21350.11340.18680.02780.3308-0.12230.47250.5442-0.1173-0.28270.152-0.03520.304-0.0117-0.30452.04571.6891-7.8795
102.58480.40540.30372.1447-0.62640.3720.2220.33880.54420.03790.10020.41280.2198-0.0766-0.3222-0.2762-0.0065-0.12580.2510.1520.048615.530110.6687-0.0208
115.84970.52182.91045.81390.03372.3142-0.01680.54420.0597-0.41950.30050.53890.5442-0.1197-0.2837-0.1382-0.152-0.1520.3040.152-0.29726.7507-10.1353-4.763
127.98850.49192.91043.3504-1.60592.97070.03390.5442-0.1549-0.0599-0.1744-0.3679-0.04720.11550.14060.2193-0.0228-0.089-0.1102-0.0554-0.30431.0248-27.230612.3684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* G|* }A-2 - 10
2X-RAY DIFFRACTION1{ A|* G|* }G7 - 12
3X-RAY DIFFRACTION2{ C|* D|* }C-2 - 10
4X-RAY DIFFRACTION2{ C|* D|* }D7 - 12
5X-RAY DIFFRACTION3{ E|1 - E|131 }E1 - 131
6X-RAY DIFFRACTION4{ E|132 - E|327 }E132 - 327
7X-RAY DIFFRACTION5{ E|328 - E|532 }E328 - 532
8X-RAY DIFFRACTION6{ E|533 - E|610 }E533 - 610
9X-RAY DIFFRACTION7{ E|611 - E|780 }E611 - 780
10X-RAY DIFFRACTION8{ F|1 - F|131 }F1 - 131
11X-RAY DIFFRACTION9{ F|132 - F|327 }F132 - 327
12X-RAY DIFFRACTION10{ F|328 - F|532 }F328 - 532
13X-RAY DIFFRACTION11{ F|533 - F|610 }F533 - 610
14X-RAY DIFFRACTION12{ F|611 - F|780 }F611 - 780

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