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- PDB-7b06: TgoT_RT521 apo -

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Basic information

Entry
Database: PDB / ID: 7b06
TitleTgoT_RT521 apo
ComponentsDNA 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
Biological speciesThermococcus gorgonarius (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 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 18, 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


Theoretical massNumber of molelcules
Total (without water)89,9211
Polymers89,9211
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.530, 109.850, 111.300
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: 89921.328 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 400, 0.1 M sodium acetate pH4.6 and 0.2M MgCl2

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.972 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.34→43.69 Å / Num. obs: 36488 / % possible obs: 99.08 % / Redundancy: 3.5 % / Biso Wilson estimate: 62.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.69
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 1.565 / Num. unique obs: 3526 / CC1/2: 0.486

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Processing

Software
NameVersionClassification
HKL-2000data 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: 2.349→43.69 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.341 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1825 5 %RANDOM
Rwork0.2249 ---
obs0.226 36488 99.3 %-
Displacement parametersBiso max: 199.74 Å2 / Biso mean: 95.01 Å2 / Biso min: 30.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.9611 Å20 Å20 Å2
2---7.5962 Å20 Å2
3---11.5573 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.349→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5641 0 0 118 5759
Biso mean---60.15 -
Num. residues----685
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2081SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes966HARMONIC5
X-RAY DIFFRACTIONt_it5768HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion724SEMIHARMONIC5
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_contact4446SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5768HARMONIC20.005
X-RAY DIFFRACTIONt_angle_deg7776HARMONIC20.75
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.04
LS refinement shellResolution: 2.35→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2559 37 5.07 %
Rwork0.2512 693 -
all0.2514 730 -
obs--92.15 %
Refinement TLS params.

T11: 0.304 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23681.1381-2.77743.2605-1.15915.8934-0.07140.1079-0.27630.05950.0290.19930.5442-0.33130.04240.0539-0.0326-0.2657-0.0231-0.304-18.0008-7.0125-7.3182
22.76780.4673-0.18375.8089-0.17827.103-0.11630.18530.5442-0.2990.2340.3885-0.5442-0.0783-0.1177-0.152-0.0104-0.15640.0441-0.1929-7.714624.8486-25.3831
31.36820.0827-1.45492.78980.85516.38450.1053-0.16380.33340.23190.089-0.0624-0.47830.4324-0.19430.0016-0.0037-0.19070.0047-0.2817-13.357215.879411.4152
42.83082.8932-0.13958.3155-1.12466.61570.1664-0.03370.54420.4715-0.1987-0.5442-0.43740.54420.0322-0.152-0.02380.27840.08930.304-6.430236.933320.4048
58.3155-0.58090.79588.3155-0.52228.31550.04960.37840.0581-0.1648-0.29610.1613-0.2342-0.17030.2464-0.08240.00270.3040.07170.304-13.062758.11582.1043
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|613 - A|755 }A613 - 755

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