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- PDB-2q2e: Crystal structure of the topoisomerase VI holoenzyme from Methano... -

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Basic information

Entry
Database: PDB / ID: 2q2e
TitleCrystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei
Components
  • Type 2 DNA topoisomerase 6 subunit B
  • Type II DNA topoisomerase VI subunit A
KeywordsISOMERASE / topoisomerase / DNA-binding / Spo11 / ATPase
Function / homology
Function and homology information


DNA endonuclease activity, producing 3'-phosphomonoesters / : / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA unwinding involved in DNA replication / DNA topological change / chromosome / magnesium ion binding / DNA binding / ATP binding
Similarity search - Function
Immunoglobulin-like - #2960 / Arc Repressor Mutant, subunit A - #80 / DNA topoisomerase VI, subunit B, C-terminal / Type 2 DNA topoisomerase 6 subunit B C-terminal domain / DNA topoisomerase VI, subunit A / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily / Type IIB DNA topoisomerase ...Immunoglobulin-like - #2960 / Arc Repressor Mutant, subunit A - #80 / DNA topoisomerase VI, subunit B, C-terminal / Type 2 DNA topoisomerase 6 subunit B C-terminal domain / DNA topoisomerase VI, subunit A / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily / Type IIB DNA topoisomerase / DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Arc Repressor Mutant, subunit A / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helicase, Ruva Protein; domain 3 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Histidine kinase/HSP90-like ATPase superfamily / Special / Ribosomal protein S13-like, H2TH / Arc Repressor Mutant, subunit A / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type 2 DNA topoisomerase 6 subunit A / Type 2 DNA topoisomerase 6 subunit B
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4 Å
AuthorsCorbett, K.D. / Benedetti, P. / Berger, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI
Authors: Corbett, K.D. / Benedetti, P. / Berger, J.M.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Type II DNA topoisomerase VI subunit A
B: Type 2 DNA topoisomerase 6 subunit B


Theoretical massNumber of molelcules
Total (without water)111,0332
Polymers111,0332
Non-polymers00
Water00
1
A: Type II DNA topoisomerase VI subunit A
B: Type 2 DNA topoisomerase 6 subunit B

A: Type II DNA topoisomerase VI subunit A
B: Type 2 DNA topoisomerase 6 subunit B


Theoretical massNumber of molelcules
Total (without water)222,0654
Polymers222,0654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Unit cell
Length a, b, c (Å)227.812, 227.812, 208.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological assembly (A2B2 heterotetramer) is generated by the two-fold axis: -y, -x, 1/3-z

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Components

#1: Protein Type II DNA topoisomerase VI subunit A


Mass: 42179.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: top6A / Plasmid: pST39 coexpression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8PUB7, EC: 5.99.1.3
#2: Protein Type 2 DNA topoisomerase 6 subunit B / Type II DNA topoisomerase VI subunit B / TopoVI-B


Mass: 68853.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: top6B / Plasmid: pST39 coexpression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8PUB8, EC: 5.99.1.3

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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: 7.04 Å3/Da / Density % sol: 82.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM sodium cacodylate pH 6.0, 1.6-1.8 M ammonium sulfate pH 7.5, 10 mM magnesium chloride, 10 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159, 1.2386, 1.21495, 1.21434
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2006
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
21.23861
31.214951
41.214341
ReflectionResolution: 4→100 Å / Num. all: 25975 / Num. obs: 25975 / % possible obs: 95.2 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.091 / Net I/σ(I): 9.1
Reflection shellResolution: 4→4.22 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.548 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0026refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 4→30 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.848 / SU B: 119.896 / SU ML: 0.733 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.68 / ESU R Free: 0.776 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34927 1269 4.9 %RANDOM
Rwork0.30579 ---
obs0.3079 24582 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1.6 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 192.573 Å2
Baniso -1Baniso -2Baniso -3
1-5.89 Å22.95 Å20 Å2
2--5.89 Å20 Å2
3----8.84 Å2
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 0 0 7039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_mcbond_it0.009543
X-RAY DIFFRACTIONr_mcangle_it1.73812
LS refinement shellResolution: 4→4.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 115 -
Rwork0.454 1757 -
obs--95.75 %
Refinement TLS params.

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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.80162.942-0.65612.61280.55823.49550.23590.10730.49630.24530.18730.469-0.0089-0.6231-0.42310.11630.3150.2384-0.25130.53580.4196-50.4479190.1187125.9162
22.9450.80251.63031.15361.79953.5842-0.150.1632-0.35470.1438-0.29870.5324-0.6133-0.39130.44880.17220.13390.57760.03130.27750.6306-67.6238179.5184148.8976
36.1589-0.2320.72775.817-1.06870.2726-0.11740.0528-0.03991.66220.18170.1233-0.67950.4515-0.06430.312-0.29490.37840.14450.21970.2219-56.1045168.1269162.9211
42.2171-0.66550.06520.6585-0.3671.8772-0.3704-0.0342-0.18320.20780.4286-0.0523-0.0120.2294-0.0582-0.17410.12530.1332-0.0594-0.0108-0.23722.9651140.3869121.077
50.1263-0.32860.62763.13311.86628.4936-0.2705-0.1020.30161.23750.407-0.6343-0.12720.423-0.13640.12920.0634-0.48160.6409-0.01850.405629.9497159.6823141.0197
62.5571-1.88780.24692.3718-0.62730.2263-0.2998-0.09160.31260.33790.4593-0.0762-0.32970.0837-0.1595-0.01160.20970.0048-0.06750.0217-0.1668-10.5378173.869125.5228
71.387-0.626-0.63945.9551-1.90823.7617-0.0474-0.05560.29960.26330.36470.2445-0.5436-0.2539-0.3172-0.14680.05430.0578-0.28860.22530.0753-26.6733216.6375106.0754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 14415 - 144
2X-RAY DIFFRACTION2AA145 - 287145 - 287
3X-RAY DIFFRACTION3AA288 - 367288 - 367
4X-RAY DIFFRACTION4BB17 - 23017 - 230
5X-RAY DIFFRACTION5BB231 - 316231 - 316
6X-RAY DIFFRACTION6BB317 - 510317 - 510
7X-RAY DIFFRACTION7BB511 - 605511 - 605

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