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- PDB-1sc7: Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoq... -

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Basic information

Entry
Database: PDB / ID: 1sc7
TitleHuman DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex
Components
  • 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
  • DNA topoisomerase ITopoisomerase
KeywordsISOMERASE/DNA / COMPLEX (ISOMERASE-DNA) / DNA / TOPOISOMERASE I / DRUG / POISON / IDENOISOQUINOLINE / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation / P-body / protein-DNA complex / circadian regulation of gene expression / fibrillar center / circadian rhythm / single-stranded DNA binding / chromosome / perikaryon / double-stranded DNA binding / peptidyl-serine phosphorylation / DNA replication / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / phosphorylation / protein serine/threonine kinase activity / chromatin binding / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain ...Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain / Topoisomerase I C-terminal domain / DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily / Eukaryotic DNA topoisomerase I, DNA binding fragment / C-terminal topoisomerase domain / DNA Topoisomerase I (eukaryota) / 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 / Topoisomerase I; Chain A, domain 4 / Beta Complex / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-M38 / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStaker, B.L. / Feese, M.D. / Cushman, M. / Pommier, Y. / Zembower, D. / Stewart, L. / Burgin, A.B.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex
Authors: Staker, B.L. / Feese, M.D. / Cushman, M. / Pommier, Y. / Zembower, D. / Stewart, L. / Burgin, A.B.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'
C: 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
A: DNA topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2446
Polymers83,7164
Non-polymers5282
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)260.940, 74.659, 57.494
Angle α, β, γ (deg.)90.00, 96.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'


Mass: 3061.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'


Mass: 3716.518 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'


Mass: 6690.362 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#4: Protein DNA topoisomerase I / Topoisomerase


Mass: 70248.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-M38 / 4-(5,11-DIOXO-5H-INDENO[1,2-C]ISOQUINOLIN-6(11H)-YL)BUTANOATE


Mass: 333.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15NO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: PEG 8000, AMMONIUM SULFATE, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2AMMONIUM SULFATE11
3MES11
4AMMONIUM SULFATE12
5MES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 18923 / % possible obs: 90.1 % / Rsym value: 0.096 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 1224 / Rsym value: 0.327 / % possible all: 32.7

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1029408.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1908 9.8 %RANDOM
Rwork0.233 ---
obs-19449 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.314251 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å2-0.33 Å2
2--18.44 Å20 Å2
3----13.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 892 38 0 5629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d6.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it2.72
X-RAY DIFFRACTIONc_scangle_it4.552.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 250 9.3 %
Rwork0.325 2432 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5M38_PAR.PARM38_TOP.TOP

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