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- PDB-8df8: Structure of M. kandleri topoisomerase V in complex with DNA. 40 ... -

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Basic information

Entry
Database: PDB / ID: 8df8
TitleStructure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex
Components
  • (DNA (42-MER)) x 2
  • 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
: / PHOSPHITE ION / PHOSPHATE ION / DNA / DNA (> 10) / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 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 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 (42-MER)
V: DNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,77714
Polymers220,0834
Non-polymers69410
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.941, 120.941, 497.569
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 3 through 324 or resid 326 through 852))
d_2ens_1(chain "B" and (resid 3 through 324 or resid 326 through 852))
d_1ens_2(chain "U" and (resid 4 through 12 or resid 15 through 26 or resid 29 through 40 or resid 42))
d_2ens_2(chain "V" and (resid 4 through 12 or resid 15 through 26 or resid 29 through 40 or resid 42))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUSERA1 - 322
d_12ens_1ILEGLYA324 - 850
d_21ens_1LEUSERB1 - 322
d_22ens_1ILEGLYB324 - 850
d_11ens_2DCDAJ
d_12ens_2PO3PO3K
d_21ens_2DCDAL
d_22ens_2PO3PO3M

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.92449898789, -0.0911435347928, 0.370127650218), (-0.121900223627, -0.84931265209, -0.513622774495), (0.361167491436, -0.51996237851, 0.774078269986)87.9902242394, -21.4282802726, -24.2533813123
2given(-0.996147594767, 0.00270622282682, 0.08765070335), (-0.0280177635477, -0.956956785052, -0.288874914919), (0.0830961753965, -0.290217828366, 0.953346022036)100.425350655, -38.1662470331, -10.1945068898

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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 , 2 types, 2 molecules UV

#2: DNA chain DNA (42-MER)


Mass: 12915.303 Da / Num. of mol.: 1 / Mutation: GUA U13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (42-MER)


Mass: 12946.312 Da / Num. of mol.: 1 / Mutation: GUA V13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 10 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3

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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: 4.14 Å3/Da / Density % sol: 70.29 % / Description: Box-like
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: 2 ul:1 ul (reaction:well solution), 2% PEG 8K, 24 mM sodium acetate pH 5.1, 26 mM sodium acetate pH 5.6, 12.5 uM phosphotungstic acid. 5X DNA binding buffer: 250 mM sodium acetate pH 5.0 at 65C, 150 mM sodium chloride, 5 mM magnesium chloride.

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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: Nov 4, 2020 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.92→108.8 Å / Num. obs: 56136 / % possible obs: 69 % / Redundancy: 13.9 % / Biso Wilson estimate: 96.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.084 / Net I/σ(I): 21
Reflection shellResolution: 2.92→3.24 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 51701 / CC1/2: 0.744 / Rrim(I) all: 1.65 / % possible all: 12.9

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.1_4122refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DF7

8df7


Resolution: 2.92→58.76 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2877 2845 5.07 %
Rwork0.2571 53278 -
obs0.2587 56123 68.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.65 Å2
Refinement stepCycle: LAST / Resolution: 2.92→58.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13604 1554 32 0 15190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002215631
X-RAY DIFFRACTIONf_angle_d0.489321412
X-RAY DIFFRACTIONf_chiral_restr0.03712375
X-RAY DIFFRACTIONf_plane_restr0.00342534
X-RAY DIFFRACTIONf_dihedral_angle_d18.63796235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.2190249189
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS2.57659256871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.970.260820.435516X-RAY DIFFRACTION0.45
2.97-3.030.546110.4113112X-RAY DIFFRACTION3.09
3.03-3.080.5788230.4495480X-RAY DIFFRACTION12.68
3.08-3.150.5255280.4092671X-RAY DIFFRACTION17.58
3.15-3.220.3593450.3894919X-RAY DIFFRACTION24.06
3.22-3.290.4056800.3931342X-RAY DIFFRACTION35.42
3.29-3.370.409960.37171787X-RAY DIFFRACTION46.82
3.37-3.460.38311000.35432272X-RAY DIFFRACTION59.18
3.46-3.570.35071720.34082933X-RAY DIFFRACTION76.93
3.57-3.680.38071890.32963583X-RAY DIFFRACTION94.65
3.68-3.810.32722060.32233840X-RAY DIFFRACTION100
3.81-3.960.34062070.29473828X-RAY DIFFRACTION99.98
3.97-4.150.32412340.28693818X-RAY DIFFRACTION99.98
4.15-4.360.28931900.27193874X-RAY DIFFRACTION100
4.36-4.640.27832160.25663864X-RAY DIFFRACTION99.95
4.64-4.990.29892170.24693865X-RAY DIFFRACTION99.95
4.99-5.50.32882270.25283921X-RAY DIFFRACTION99.93
5.5-6.290.28541890.27053951X-RAY DIFFRACTION99.95
6.29-7.920.27981980.22994009X-RAY DIFFRACTION99.95
7.92-58.760.19482150.18264193X-RAY DIFFRACTION98.57

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