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- PDB-4gfh: Topoisomerase II-DNA-AMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 4gfh
TitleTopoisomerase II-DNA-AMPPNP complex
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
  • DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')
  • DNA topoisomerase 2Topoisomerase
KeywordsIsomerase/DNA / TOPOISOMERASE / PROTEIN-DNA COMPLEX / DNA SUPERCOILING / DNA REPLICATION / ATP-BINDING / DNA-BINDING / ISOMERASE / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ...replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / rRNA transcription / DNA topological change / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus
Similarity search - Function
DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV ...DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA topoisomerase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.408 Å
AuthorsSchmidt, B.H. / Osheroff, N. / Berger, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
Authors: Schmidt, B.H. / Osheroff, N. / Berger, J.M.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 31, 2019Group: Data collection / Derived calculations / Category: chem_comp / struct_conn / Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2
B: DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
C: DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
D: DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
F: DNA topoisomerase 2
G: DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
H: DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
I: DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')
J: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,57814
Polymers304,51710
Non-polymers1,0614
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.135, 169.884, 169.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS A DIMER

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein DNA topoisomerase 2 / Topoisomerase / DNA topoisomerase II


Mass: 136355.125 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-1177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TOP2, TOR3, YNL088W, N2244 / References: UniProt: P06786, EC: 5.99.1.3

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DNA chain , 4 types, 8 molecules BGCHDIEJ

#2: DNA chain DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')


Mass: 3269.149 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')


Mass: 4675.035 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')


Mass: 3429.312 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')


Mass: 4529.949 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG 300, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2010
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 4.408→50 Å / Num. all: 28660 / Num. obs: 28660 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 4.408→4.57 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.703 / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.408→46.988 Å / SU ML: 0.54 / σ(F): 1.33 / Phase error: 30.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 1450 5.06 %random
Rwork0.2391 ---
obs0.241 28660 91.22 %-
all-28660 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 187.65 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.3384 Å2-0 Å20 Å2
2--2.357 Å2-0 Å2
3---5.9815 Å2
Refinement stepCycle: LAST / Resolution: 4.408→46.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18054 2118 64 0 20236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420878
X-RAY DIFFRACTIONf_angle_d0.84228615
X-RAY DIFFRACTIONf_dihedral_angle_d15.7948059
X-RAY DIFFRACTIONf_chiral_restr0.0543120
X-RAY DIFFRACTIONf_plane_restr0.0043269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.408-4.56520.42171180.36962690X-RAY DIFFRACTION90
4.5652-4.74780.37391410.33092707X-RAY DIFFRACTION93
4.7478-4.96370.33031480.29662718X-RAY DIFFRACTION92
4.9637-5.22510.33131450.28172722X-RAY DIFFRACTION93
5.2251-5.55190.32671420.26552749X-RAY DIFFRACTION92
5.5519-5.97980.34731460.27192738X-RAY DIFFRACTION92
5.9798-6.58010.33711440.26722692X-RAY DIFFRACTION91
6.5801-7.52890.24621650.22312690X-RAY DIFFRACTION90
7.5289-9.47290.24391470.18062745X-RAY DIFFRACTION91
9.4729-46.9880.22211540.20742759X-RAY DIFFRACTION88
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)
12.87330.8298-0.02913.152-0.79220.41720.2541-1.3744-0.36670.9153-0.5053-0.2056-0.42211.07660.18221.7641-0.1245-0.17741.78270.31290.99827.892821.619175.5921
25.38052.78330.98075.03893.33434.16160.521-0.2556-0.31240.1966-0.78260.4485-0.4555-0.20770.2522.0154-0.0320.36271.49870.12692.0684-5.312311.292450.8516
33.9642.04251.64973.02763.06314.5942-0.29810.43020.1071-1.06450.3945-0.0497-0.85250.9176-0.01791.861-0.1578-0.34792.06480.07531.9909-12.106129.1108-6.0183
42.57380.58351.4621.281.06432.95430.0752-0.41360.30220.2244-0.445-0.07830.22750.0530.43661.87670.0013-0.16571.5481-0.13871.7032-48.81643.06171.794
53.62532.58674.81042.78191.95098.5573-0.74690.31571.2027-0.6636-0.65680.56051.09090.17441.18751.50710.1149-0.25591.8246-0.03521.8533-22.892742.689115.0696
63.14951.29380.20685.2606-3.11382.64680.56651.1084-0.24821.84340.20311.96870.41210.7006-0.71862.2195-0.23510.22081.4538-0.17711.5332-24.029439.262316.5929
74.8443-3.12764.8932.8248-4.28776.29331.1707-0.22961.2729-0.4032-0.96580.65991.01621.4999-0.09491.7557-0.0889-0.34172.2403-0.01451.2271-27.1749-0.245519.4257
81.57092.17690.03733.21430.49732.4254-0.1550.16550.1724-0.79710.31290.2052-0.6133-1.08220.07982.26790.2553-0.08961.81440.20032.3839-25.69143.135218.2475
91.12250.7442-0.24613.2783-1.58941.92740.4277-1.1111-0.4625-0.1922-0.612-0.8802-0.11671.1460.19120.9798-0.2805-0.22821.7320.0861.82633.300220.892250.2072
103.6033-2.59591.20345.0811-1.68645.18740.1898-0.0651-0.4335-0.3233-0.4895-0.6295-0.77940.32280.55472.2196-0.17930.36051.40770.18412.00619.214231.346237.1597
113.2841-1.44381.76211.4558-1.95113.3358-0.1747-0.7443-0.50510.67640.38850.7421-0.1051-0.3267-0.252.31230.0921-0.38742.43160.07862.2724-48.295613.347730.1698
123.8392-1.63811.71191.2971-0.51523.20550.4004-0.09830.3988-0.0479-0.3988-0.42450.21910.38380.02931.56980.0776-0.1931.2787-0.04761.7945-40.4565-0.5927-6.5379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 7:240)
2X-RAY DIFFRACTION2chain A and (resseq 241:408)
3X-RAY DIFFRACTION3chain A and (resseq 421:690)
4X-RAY DIFFRACTION4chain A and (resseq 691:1177)
5X-RAY DIFFRACTION5chain B or chain D
6X-RAY DIFFRACTION6chain C or chain E
7X-RAY DIFFRACTION7chain G or chain I
8X-RAY DIFFRACTION8chain H or chain J
9X-RAY DIFFRACTION9chain F and (resseq 7:240)
10X-RAY DIFFRACTION10chain F and (resseq 241:404)
11X-RAY DIFFRACTION11chain F and (resseq 421:690)
12X-RAY DIFFRACTION12chain F and (resseq 691:1177)

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