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- PDB-8df9: Structure of M. kandleri topoisomerase V in complex with DNA. 38 ... -

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Basic information

Entry
Database: PDB / ID: 8df9
TitleStructure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA complex
Components
  • (DNA (33-MER)) x 2
  • DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
  • Topoisomerase V
KeywordsDNA BINDING PROTEIN/DNA / Topoisomerase V Type IC / Abasic DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


isomerase activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA topoisomerase V, catalytic domain superfamily / : / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain ...DNA topoisomerase V, catalytic domain superfamily / : / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.24 Å
AuthorsOsterman, A. / Mondragon, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118108 United States
CitationJournal: Elife / Year: 2022
Title: Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
Authors: Osterman, A. / Mondragon, A.
History
DepositionJun 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Topoisomerase V
B: Topoisomerase V
S: DNA (33-MER)
T: DNA (33-MER)
U: DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')
V: DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
W: DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')
X: DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,87922
Polymers237,5098
Non-polymers37014
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.751, 193.751, 245.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 828 or resid 835 through 852))
d_2ens_1(chain "B" and (resid 2 through 617 or resid 690 through 852))
d_1ens_2chain "U"
d_2ens_2(chain "W" and resid 2 through 18)
d_1ens_3(chain "V" and (resid 20 through 38 or (resid 39...
d_2ens_3chain "X"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA1 - 755
d_12ens_1ALAGLYA762 - 779
d_21ens_1ALALYSB1 - 616
d_22ens_1GLUGLYB689 - 845
d_11ens_2DGDCQ
d_21ens_2DGDCS
d_11ens_3DTDTR
d_21ens_3DTDTT

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.990067428864, 0.0517304157731, -0.13073044935), (-0.0948326369972, 0.440749583972, 0.892606618387), (0.103794302655, 0.896138252901, -0.431466075635)14.9656118676, -5.17135139595, 1.98877755996
2given(0.011385798483, 0.910446436547, -0.413470252585), (0.825018809348, 0.225083690038, 0.518344766252), (0.564990555509, -0.347022504542, -0.748572677518)59.3577305808, -14.8968441407, -83.3371892737
3given(0.0530424250418, 0.88040200818, -0.471252379451), (0.850202655929, 0.207712052243, 0.483746986766), (0.52377661746, -0.426319137907, -0.737502574678)53.2811716879, -17.5963537474, -87.7734176536

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Topoisomerase V / Winged helix-turn-helix transcriptional regulator


Mass: 97110.445 Da / Num. of mol.: 2 / Mutation: K809A, K820A, K831A, K835A, K846A, K851A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: top5, HA336_03250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q977W1

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DNA chain , 5 types, 6 molecules STUVXW

#2: DNA chain DNA (33-MER)


Mass: 10203.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (33-MER)


Mass: 10096.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3')


Mass: 5221.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3')


Mass: 6115.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3')


Mass: 5534.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 44 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.87 Å3/Da / Density % sol: 74.76 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. ...Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. Crystals started to appear within minutes of setting up the trays in 1:1 or 2:1 well to complex ratio. Well solution: 10% PEG 600, 50 mM sodium succinate pH 5.5, 200 mM potassium chloride, 10 mM magnesium chloride, 1 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 14, 2018 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.24→39.3 Å / Num. obs: 52587 / % possible obs: 70.4 % / Redundancy: 8.2 % / Biso Wilson estimate: 121.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.1 / Net I/σ(I): 13.5
Reflection shellResolution: 3.24→3.601 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2629 / CC1/2: 0.58 / Rrim(I) all: 1.567 / % possible all: 13.2

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.1_4122refinement
XDSdata reduction
STARANISOdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.24→39.28 Å / SU ML: 0.3447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 2599 4.95 %
Rwork0.2346 49867 -
obs0.2362 52466 70.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 141.21 Å2
Refinement stepCycle: LAST / Resolution: 3.24→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13014 2871 44 0 15929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003916442
X-RAY DIFFRACTIONf_angle_d0.561722799
X-RAY DIFFRACTIONf_chiral_restr0.0372523
X-RAY DIFFRACTIONf_plane_restr0.00412483
X-RAY DIFFRACTIONf_dihedral_angle_d20.86756559
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.83125288934
ens_2d_2UX-RAY DIFFRACTIONTorsion NCS1.27918545827
ens_3d_2VX-RAY DIFFRACTIONTorsion NCS2.12223141682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.30.288130.471295X-RAY DIFFRACTION2.56
3.3-3.360.3256110.5044216X-RAY DIFFRACTION5.93
3.36-3.430.398220.434350X-RAY DIFFRACTION9.62
3.43-3.510.3665320.3623702X-RAY DIFFRACTION19.03
3.51-3.590.389600.3661952X-RAY DIFFRACTION26.16
3.59-3.680.3246720.31431398X-RAY DIFFRACTION38.05
3.68-3.780.34041170.29951913X-RAY DIFFRACTION52.31
3.78-3.890.32231490.29322890X-RAY DIFFRACTION78.16
3.89-4.010.3011910.28793660X-RAY DIFFRACTION98.62
4.01-4.160.28041810.27023699X-RAY DIFFRACTION100
4.16-4.320.25442110.24613701X-RAY DIFFRACTION100
4.32-4.520.25111790.23933722X-RAY DIFFRACTION99.97
4.52-4.760.27331990.22713720X-RAY DIFFRACTION100
4.76-5.060.28951630.22783765X-RAY DIFFRACTION100
5.06-5.450.25212000.23883726X-RAY DIFFRACTION100
5.45-5.990.28411800.26373789X-RAY DIFFRACTION100
5.99-6.860.27252290.25863773X-RAY DIFFRACTION100
6.86-8.620.24021840.21543844X-RAY DIFFRACTION100
8.62-39.280.24252160.18773952X-RAY DIFFRACTION98.53

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