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- PDB-7b0g: TgoT_6G12 binary with 2 hCTPs -

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Basic information

Entry
Database: PDB / ID: 7b0g
TitleTgoT_6G12 binary with 2 hCTPs
Components
  • DNA (5'-D(P*AP*TP*TP*GP*GP*CP*TP*GP*CP*CP*CP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*GP*GP*GP*CP*AP*GP*()P*())-3')
  • DNA polymerase
KeywordsDNA BINDING PROTEIN / archaea / polymerase
Function / homology
Function and homology information


exonuclease activity / DNA-templated 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 / : / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / 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 Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / : / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / 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 polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus gorgonarius (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,2966
Polymers96,6233
Non-polymers6733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-21 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.210, 106.770, 231.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (E. coli) / References: UniProt: P56689, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*GP*CP*AP*GP*()P*())-3')


Mass: 3452.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*GP*GP*CP*TP*GP*CP*CP*CP*TP*CP*C)-3')


Mass: 3286.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Has protein modificationY

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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: 3.62 Å3/Da / Density % sol: 66.05 %
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: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→49.74 Å / Num. obs: 28838 / % possible obs: 99.88 % / Redundancy: 2.8 % / Biso Wilson estimate: 131.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2038 / Net I/σ(I): 9.21
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 3.171 / Num. unique obs: 2829 / CC1/2: 0.292

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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→49.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 1.047 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.028 / SU Rfree Blow DPI: 0.34 / SU Rfree Cruickshank DPI: 0.345
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1442 5 %RANDOM
Rwork0.2251 ---
obs0.226 28838 100 %-
Displacement parametersBiso max: 233.68 Å2 / Biso mean: 128.47 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--19.0469 Å20 Å20 Å2
2--14.5505 Å20 Å2
3---4.4964 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 3→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6059 453 23 0 6535
Biso mean--182.6 --
Num. residues----759
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2349SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1072HARMONIC5
X-RAY DIFFRACTIONt_it6726HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion845SEMIHARMONIC5
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_contact4657SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6726HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg9167HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion18.19
LS refinement shellResolution: 3→3.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3249 29 5.03 %
Rwork0.266 548 -
all0.2688 577 -
obs--99.48 %
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)
11.89581.7492-1.55212.3838-0.00371.97540.0022-0.0584-0.022-0.5442-0.1029-0.12660.1833-0.06530.10070.22130.1440.152-0.16280.0184-0.0788-0.238416.9755-65.3645
20.55960.2061-2.4815.9384-0.70543.1146-0.11390.0145-0.13140.5442-0.19140.16340.17770.09950.3053-0.0021-0.07580.152-0.1144-0.07330.0064-18.827-0.7349-36.6021
30.03610.3727-0.30422.22140.15062.11240.0290.0811-0.13830.0159-0.17240.0293-0.34380.08790.1434-0.07910.05080.07930.01550.02590.0273-3.906335.2568-41.5569
40.9926-1.299-2.075.4325-0.10985.337-0.0257-0.32220.07670.54420.28770.4641-0.5442-0.1957-0.2620.3040.08520.152-0.08980.0435-0.304-9.926945.0381-19.7495
50.0422-1.73050.95140.8159-2.17885.05630.1999-0.081-0.347-0.17530.1444-0.1040.036-0.478-0.34430.303-0.1520.03480.13160.1022-0.304-4.527820.88322.5457
60-2.5598-2.36237.5143-2.91047.0058-0.0953-0.5442-0.54420.5442-0.0984-0.04840.21910.54420.19370.0642-0.14-0.1520.05870.152-0.17455.173625.2268-23.3024
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 }A328 - 532
4X-RAY DIFFRACTION4{ A|533 - A|610 }A533 - 610
5X-RAY DIFFRACTION5{ A|611 - A|769 }A611 - 769
6X-RAY DIFFRACTION6{ P|* T|* }P4 - 14
7X-RAY DIFFRACTION6{ P|* T|* }T3 - 13

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