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- PDB-8df7: Structure of M. kandleri topoisomerase V in complex with DNA. 38 ... -

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Basic information

Entry
Database: PDB / ID: 8df7
TitleStructure of M. kandleri topoisomerase V in complex with DNA. 38 base pair symmetric DNA complex
Components
  • DNA (39-MER)
  • 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: 3.52 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 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Topoisomerase V
B: Topoisomerase V
U: DNA (39-MER)
V: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,4049
Polymers218,2084
Non-polymers1955
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.665, 121.665, 498.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#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 4 through 36 or resid 38...
d_2ens_1(chain "B" and (resid 4 through 36 or resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALTHRA2 - 34
d_12ens_1TYRALAA36 - 241
d_13ens_1ARGMETA243 - 284
d_14ens_1ARGARGA286
d_15ens_1LEUASPA288 - 301
d_16ens_1TYRSERA303 - 322
d_17ens_1ILETYRA324 - 329
d_18ens_1THRGLUA331 - 387
d_19ens_1METPROA389 - 630
d_110ens_1LEUGLUA632 - 668
d_111ens_1VALARGA670 - 681
d_112ens_1SERGLYA684 - 685
d_113ens_1GLUASPA688 - 740
d_114ens_1ALAALAA742 - 796
d_115ens_1ILEARGA798 - 819
d_116ens_1TYRVALA821 - 827
d_117ens_1ALAGLYA829 - 850
d_21ens_1VALTHRB2 - 34
d_22ens_1TYRALAB36 - 241
d_23ens_1ARGMETB243 - 284
d_24ens_1ARGARGB286
d_25ens_1LEUASPB288 - 301
d_26ens_1TYRSERB303 - 322
d_27ens_1ILETYRB324 - 329
d_28ens_1THRGLUB331 - 387
d_29ens_1METPROB389 - 630
d_210ens_1LEUGLUB632 - 668
d_211ens_1VALARGB670 - 681
d_212ens_1SERGLYB684 - 685
d_213ens_1GLUASPB688 - 740
d_214ens_1ALAALAB742 - 796
d_215ens_1ILEARGB798 - 819
d_216ens_1TYRVALB821 - 827
d_217ens_1ALAGLYB829 - 850

NCS oper: (Code: givenMatrix: (-0.927272688783, -0.0898130683961, 0.363454224605), (-0.11843596369, -0.850572044472, -0.512347655081), (0.355159517883, -0.518132039067, 0.778075129373)Vector: 87. ...NCS oper: (Code: given
Matrix: (-0.927272688783, -0.0898130683961, 0.363454224605), (-0.11843596369, -0.850572044472, -0.512347655081), (0.355159517883, -0.518132039067, 0.778075129373)
Vector: 87.842428706, -21.9916943965, -24.0946747463)

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Components

#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
#2: DNA chain DNA (39-MER)


Mass: 11993.710 Da / Num. of mol.: 2 / Mutation: GUA U13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
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: 4.24 Å3/Da / Density % sol: 70.97 % / Description: Box-like
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.1
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: 2% PEG 8K, 24 mM sodium acetate pH 5.1, 26 mM sodium acetate pH 5.5, 12.5 uM phosphotungstic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 13, 2019 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.52→59.1 Å / Num. obs: 41745 / % possible obs: 87.5 % / Redundancy: 9.5 % / Biso Wilson estimate: 107.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.128 / Net I/σ(I): 12
Reflection shellResolution: 3.52→3.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 13495 / CC1/2: 0.633 / Rrim(I) all: 1.289 / % possible all: 28.2

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.1_4122refinement
XDSdata reduction
STARANISOdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.52→59.1 Å / SU ML: 0.4193 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 2127 5.1 %
Rwork0.229 39593 -
obs0.2313 41720 87.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.74 Å2
Refinement stepCycle: LAST / Resolution: 3.52→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13604 1559 5 0 15168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001915542
X-RAY DIFFRACTIONf_angle_d0.426921272
X-RAY DIFFRACTIONf_chiral_restr0.03412359
X-RAY DIFFRACTIONf_plane_restr0.00322529
X-RAY DIFFRACTIONf_dihedral_angle_d16.23336182
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.2972136173 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.60.346790.331309X-RAY DIFFRACTION10.2
3.6-3.690.3585650.315960X-RAY DIFFRACTION32.84
3.69-3.790.36641280.27632198X-RAY DIFFRACTION74.79
3.79-3.90.33661420.25452840X-RAY DIFFRACTION95.92
3.91-4.030.33651750.24062933X-RAY DIFFRACTION99.81
4.03-4.180.29121740.22832978X-RAY DIFFRACTION99.87
4.18-4.340.24851460.21772981X-RAY DIFFRACTION99.87
4.34-4.540.25011520.19952980X-RAY DIFFRACTION99.78
4.54-4.780.25081760.2062974X-RAY DIFFRACTION99.81
4.78-5.080.26761810.20322975X-RAY DIFFRACTION99.78
5.08-5.470.2911710.22692991X-RAY DIFFRACTION99.72
5.47-6.020.30181420.24983044X-RAY DIFFRACTION99.62
6.02-6.890.33641520.25273066X-RAY DIFFRACTION99.63
6.89-8.680.23971480.22463129X-RAY DIFFRACTION99.39
8.68-59.10.23761660.22383235X-RAY DIFFRACTION97.48

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