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- PDB-8dfb: Structure of M. kandleri topoisomerase V in complex with DNA. 39 ... -

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Basic information

Entry
Database: PDB / ID: 8dfb
TitleStructure of M. kandleri topoisomerase V in complex with DNA. 39 base pair symmetric DNA complex
Components
  • (DNA (40-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
: / DNA / DNA (> 10) / Topoisomerase V
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Topoisomerase V
B: Topoisomerase V
U: DNA (40-MER)
V: DNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,9828
Polymers218,8264
Non-polymers1564
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.560, 121.560, 497.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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 ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.919729630995, -0.0967782853096, 0.380435762465), (-0.119061268388, -0.854710372544, -0.505266853688), (0.374061251989, -0.510004061316, 0.774579910146)87.9178493553, -22.4385076206, -24.9361219989
2given(-0.922868020368, -0.104247221244, 0.370738632792), (-0.108682232798, -0.853039444369, -0.51040364284), (0.369462838802, -0.511327901853, 0.775913002553)88.4946012693, -22.8191559044, -25.0244491243

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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 (40-MER)


Mass: 12297.902 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 (40-MER)


Mass: 12306.917 Da / Num. of mol.: 1 / Mutation: GUA U13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.2 Å3/Da / Density % sol: 70.69 % / 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 5.6, 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-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 5, 2021 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.17→86.9 Å / Num. obs: 53311 / % possible obs: 82.4 % / Redundancy: 8.8 % / Biso Wilson estimate: 104.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.084 / Net I/σ(I): 18.1
Reflection shellResolution: 3.17→3.36 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2667 / CC1/2: 0.646 / Rrim(I) all: 1.41 / % possible all: 25.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000262487

Resolution: 3.17→59.04 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 2690 5.05 %
Rwork0.2185 --
obs0.2202 53291 82.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.17→59.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13604 1617 4 0 15225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215608
X-RAY DIFFRACTIONf_angle_d0.44121373
X-RAY DIFFRACTIONf_dihedral_angle_d16.9686210
X-RAY DIFFRACTIONf_chiral_restr0.0352370
X-RAY DIFFRACTIONf_plane_restr0.0032532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.230.669360.3419164X-RAY DIFFRACTION5
3.23-3.290.3361320.3502664X-RAY DIFFRACTION21
3.29-3.360.3706850.3291503X-RAY DIFFRACTION48
3.36-3.420.3499960.34362005X-RAY DIFFRACTION67
3.45-3.510.33891070.31632053X-RAY DIFFRACTION83
3.51-3.60.34931730.3023049X-RAY DIFFRACTION96
3.6-3.690.40221120.30522370X-RAY DIFFRACTION74
3.69-3.80.3131740.27513200X-RAY DIFFRACTION100
3.8-3.930.27511600.26432829X-RAY DIFFRACTION89
3.93-4.070.27861790.2543174X-RAY DIFFRACTION100
4.07-4.230.29451900.24833176X-RAY DIFFRACTION100
4.23-4.420.28971450.22393234X-RAY DIFFRACTION100
4.42-4.650.24421840.20523225X-RAY DIFFRACTION100
4.65-4.940.26851820.20463217X-RAY DIFFRACTION100
4.95-5.330.26192000.21923228X-RAY DIFFRACTION100
5.33-5.860.26781660.22123267X-RAY DIFFRACTION100
5.86-6.710.27681550.22253326X-RAY DIFFRACTION100
6.71-8.450.20251610.18653359X-RAY DIFFRACTION100
8.45-59.040.16241830.15863558X-RAY DIFFRACTION99

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