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- PDB-7b0f: TgoT_6G12 Binary complex -

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Basic information

Entry
Database: PDB / ID: 7b0f
TitleTgoT_6G12 Binary complex
Components
  • DNA (5'-D(P*AP*AP*CP*GP*GP*CP*TP*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: 2.797 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 1.0Dec 30, 2020Provider: 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 polymerase
B: DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')
C: DNA (5'-D(P*AP*AP*CP*GP*GP*CP*TP*AP*AP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1514
Polymers95,6693
Non-polymers4821
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-24 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.490, 111.920, 74.100
Angle α, β, γ (deg.)90.000, 110.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA polymerase / / TO POL


Mass: 89884.258 Da / Num. of mol.: 1
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
#2: DNA chain DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')


Mass: 1784.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*CP*GP*GP*CP*TP*AP*AP*TP*GP*CP*G)-3')


Mass: 4000.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 20K and 0.1 M MES-NaOH pH6.5

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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: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.797→46.7 Å / Num. obs: 31065 / % possible obs: 99.57 % / Redundancy: 3.5 % / Biso Wilson estimate: 107.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1749 / Net I/σ(I): 7.18
Reflection shellResolution: 2.797→2.897 Å / Rmerge(I) obs: 1.737 / Num. unique obs: 3015 / CC1/2: 0.319

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Processing

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

1tgo


Resolution: 2.797→46.7 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.707 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.632 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.308
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 1554 5 %RANDOM
Rwork0.2309 ---
obs0.2315 31065 99.7 %-
Displacement parametersBiso max: 159.36 Å2 / Biso mean: 90.08 Å2 / Biso min: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1--3.5035 Å20 Å2-9.9071 Å2
2--17.1017 Å20 Å2
3----13.5982 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 2.797→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 390 13 80 6429
Biso mean--152.13 57.56 -
Num. residues----740
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2284SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1035HARMONIC5
X-RAY DIFFRACTIONt_it6530HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
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_contact4643SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6530HARMONIC20.005
X-RAY DIFFRACTIONt_angle_deg8889HARMONIC20.71
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion17.38
LS refinement shellResolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3064 31 4.98 %
Rwork0.3272 591 -
all0.3262 622 -
obs--90.69 %
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)
13.6051-0.7073-1.0114.9891-2.84064.4654-0.134-0.51790.08950.3530.23660.6123-0.10170.0189-0.1025-0.16560.03190.1243-0.2821-0.06020.0115-60.007639.897338.4095
25.11.3759-1.76927.6362-1.03872.82070.2396-0.08580.2477-0.2558-0.2622-0.6697-0.31050.45650.02260.16-0.05310.2142-0.11070.0983-0.0483-36.389358.028514.3094
32.0909-1.1914-0.25083.25030.32190.72390.03850.1221-0.2503-0.2782-0.0550.0311-0.05540.10250.0165-0.1336-0.03920.107-0.2112-0.0004-0.1083-40.76920.633825.046
46.20090.1182-2.53720.0428-0.70743.1719-0.14620.5871-0.3803-0.3798-0.02960.13690.2196-0.01750.1758-0.1199-0.04810.05870.0973-0.14520.0152-23.336511.207111.4225
54.19262.02650.21858.31552.90153.6771-0.22470.42770.36650.37240.0372-0.3795-0.722-0.25370.18740.15060.01230.14120.28730.10210.1928-0.71234.173412.2758
60.8209-1.4533-0.95178.31550.3995-0.8209-0.1757-0.11430.55310.4790.37190.2734-0.53540.12-0.19620.2477-0.07390.06530.3040.0950.3603-28.793732.469929.8125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|131 }A1 - 131
2X-RAY DIFFRACTION2{ A|132 - A|327 }A132 - 327
3X-RAY DIFFRACTION3{ A|328 - A|532 A|801 }A328 - 532
4X-RAY DIFFRACTION3{ A|328 - A|532 A|801 }A801
5X-RAY DIFFRACTION4{ A|533 - A|610 }A533 - 610
6X-RAY DIFFRACTION5{ A|613 - A|760 }A613 - 760
7X-RAY DIFFRACTION6{ B|* C|* }B7 - 12
8X-RAY DIFFRACTION6{ B|* C|* }C-2 - 10

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