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- PDB-2h7g: Structure of variola topoisomerase non-covalently bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2h7g
TitleStructure of variola topoisomerase non-covalently bound to DNA
Components
  • 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
  • 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3'
  • DNA topoisomerase 1Topoisomerase
KeywordsISOMERASE/DNA / type IB topoisomerase / dna binding / protein-dna complex / isomerase / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / virion component / DNA binding
Similarity search - Function
DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. ...DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesVariola virus (smallpox virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPerry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural basis for specificity in the poxvirus topoisomerase.
Authors: Perry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
History
DepositionJun 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3'
Z: 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
X: DNA topoisomerase 1


Theoretical massNumber of molelcules
Total (without water)44,5603
Polymers44,5603
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.181, 133.648, 112.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3'


Mass: 3604.352 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'


Mass: 4337.855 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA topoisomerase 1 / Topoisomerase / E.C.5.99.1.2 / DNA topoisomerase I


Mass: 36617.449 Da / Num. of mol.: 1 / Mutation: C100S, C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variola virus (smallpox virus) / Genus: Orthopoxvirus / Gene: TOP1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32989, DNA topoisomerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Tris-HClTris11
3H2O11
4PEG 800012
5Tris-HClTris12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38372 / % possible obs: 96.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Χ2: 1.612 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.962.10.53229450.84389.8
1.96-2.022.90.41132000.8597.7
2.02-2.093.40.32232150.9198.2
2.09-2.173.40.24131860.94197
2.17-2.273.60.1832031.03597.5
2.27-2.393.50.13531791.10196.2
2.39-2.543.60.10431811.19896.4
2.54-2.743.60.08431791.40195.7
2.74-3.023.60.0731701.65195.3
3.02-3.453.60.06231642.15594.9
3.45-4.356.10.0732532.37796.2
4.35-5010.20.06334972.05399.6

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Phasing

Phasing MRRfactor: 0.566 / Cor.coef. Fo:Fc: 0.279
Highest resolutionLowest resolution
Rotation3 Å40.9 Å
Translation3 Å40.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.197 / SU B: 6.995 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1913 5 %RANDOM
Rwork0.197 ---
all0.199 ---
obs0.199 38316 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.614 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.42 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 531 0 395 3548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223280
X-RAY DIFFRACTIONr_angle_refined_deg1.6892.1674547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92323.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02815516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5781515
X-RAY DIFFRACTIONr_chiral_restr0.1140.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022252
X-RAY DIFFRACTIONr_nbd_refined0.2160.21573
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.222
X-RAY DIFFRACTIONr_mcbond_it0.7971.51651
X-RAY DIFFRACTIONr_mcangle_it1.27622631
X-RAY DIFFRACTIONr_scbond_it2.14732003
X-RAY DIFFRACTIONr_scangle_it2.9944.51916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.3131470.2742425288889.058
1.949-2.0030.3291530.2492635284797.928
2.003-2.0610.2941380.2322537275297.202
2.061-2.1240.261420.2232470267697.608
2.124-2.1940.2771330.2172430262197.787
2.194-2.2710.2531190.2212314250497.165
2.271-2.3560.271100.2172237243696.346
2.356-2.4520.2991200.2142140235196.129
2.452-2.5610.232900.2272085225596.452
2.561-2.6860.261860.2221965214195.796
2.686-2.8310.2721010.2191863206095.34
2.831-3.0020.273890.2171762195394.777
3.002-3.2090.262800.2021655182495.121
3.209-3.4660.211900.1771552172695.133
3.466-3.7950.209700.1751412158093.797
3.795-4.2420.229610.1651358145097.862
4.242-4.8950.2550.16612141269100
4.895-5.9870.223620.19910441106100
5.987-8.4330.231340.207840874100
8.433-66.8150.249330.16146551696.512

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