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- PDB-1r49: Human topoisomerase I (Topo70) double mutant K532R/Y723F -

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Basic information

Entry
Database: PDB / ID: 1r49
TitleHuman topoisomerase I (Topo70) double mutant K532R/Y723F
Components
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
  • 5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
  • DNA topoisomerase ITopoisomerase
KeywordsIsomerase/DNA / Protein / DNA / topoisomerase I / Isomerase-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / chromosome segregation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / chromosome segregation / protein-DNA complex / P-body / 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
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsInterthal, H. / Quigley, P.M. / Hol, W.G. / Champoux, J.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The role of lysine 532 in the catalytic mechanism of human topoisomerase I.
Authors: Interthal, H. / Quigley, P.M. / Hol, W.G. / Champoux, J.J.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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*TP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
C: 5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
A: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)83,6763
Polymers83,6763
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.944, 118.638, 71.651
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6790.468 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'


Mass: 6705.373 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA topoisomerase I / Topoisomerase / 5.99.1.2


Mass: 70180.055 Da / Num. of mol.: 1 / Fragment: Topo70 / Mutation: K532R, Y723F
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 3350 MME, Magnesium chloride, MES, TCEP, pH 7.5, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2MME11
3Magnesium chloride11
4MES11
5TCEP11
6H2O11
7PEG 335012
8Magnesium chloride12
9H2O12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
148 Mprotein1drop
215 %PEG3350 MME1drop
3200 mM1dropMgCl2
4100 mMMES1droppH7.5
52 mMTCEP1drop
615 %ethylene gylcol1reservoir
71
81
91

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.13→50 Å / Num. obs: 15514 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.13→3.26 Å / Rsym value: 0.28 / % possible all: 64.7
Reflection
*PLUS
Highest resolution: 3.1 Å / Num. obs: 15497 / Redundancy: 3.2 % / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
% possible obs: 64.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→47.67 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.841 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.656 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33917 821 5.3 %RANDOM
Rwork0.27681 ---
all0.28009 ---
obs0.28009 14675 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.04 Å2
2---0.37 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 3.13→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4527 897 0 29 5453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0215560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7632.1627645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.595540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.32682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.5285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it5.6863.52725
X-RAY DIFFRACTIONr_mcangle_it9.13864394
X-RAY DIFFRACTIONr_scbond_it14.5518.82835
X-RAY DIFFRACTIONr_scangle_it19.42612.53251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.13→3.211 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.536 28
Rwork0.357 621
Refinement
*PLUS
Highest resolution: 3.1 Å / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.004
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.763

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