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- PDB-1a36: TOPOISOMERASE I/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a36
TitleTOPOISOMERASE I/DNA COMPLEX
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*A P*TP*TP*TP*TP*T)- 3')
  • DNA (5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*C P*TP*TP*TP*TP*T)- 3')
  • TOPOISOMERASE I
KeywordsISOMERASE/DNA / COMPLEX (ISOMERASE-DNA) / 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 / P-body / circadian regulation of gene expression / protein-DNA complex / fibrillar center / circadian rhythm / single-stranded DNA binding / peptidyl-serine phosphorylation / chromosome / double-stranded DNA binding / perikaryon / DNA replication / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / 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 / : / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / Yeast DNA topoisomerase - domain 1 / 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 / : / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / Yeast DNA topoisomerase - domain 1 / 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. / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / 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 / RIGID BODY REFINEMENT / Resolution: 2.8 Å
AuthorsStewart, L. / Redinbo, M.R. / Qiu, X. / Champoux, J.J. / Hol, W.G.J.
CitationJournal: Science / Year: 1998
Title: A model for the mechanism of human topoisomerase I.
Authors: Stewart, L. / Redinbo, M.R. / Qiu, X. / Hol, W.G. / Champoux, J.J.
History
DepositionJan 29, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,5193
Polymers83,5193
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.500, 118.400, 71.500
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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


Mass: 6705.373 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein TOPOISOMERASE I


Mass: 70022.859 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN AND C-TERMINAL DOMAIN / Mutation: Y723F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, EC: 5.99.1.2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNOTE THAT RESIDUES 174 - 214 AND 634 - 640 OF CHAIN A ARE DISORDERED AND ARE NOT PRESENT IN THE ...NOTE THAT RESIDUES 174 - 214 AND 634 - 640 OF CHAIN A ARE DISORDERED AND ARE NOT PRESENT IN THE MODEL. 1-22 OF CHAIN C COMPRISE THE SCISSILE STRAND OF THE DNA, 101-122 OF CHAIN D THE INTACT DNA STRAND. TER PHE 765 A IS THE C-TERMINAL RESIDUE OF THE 70 KDA FRAGMENT OF HUMAN TOPO I. THY 22 C IS THE 3' TERMINAL NUCLEOTIDE ON THE SCISSILE STRAND OF THE DNA DUPLEX. THY 122 D IS THE 3' TERMINAL NUCLEOTIDE ON THE INTACT STRAND OF THE DNA DUPLEX.

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growpH: 7.7 / Details: pH 7.70
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.2 mMTris-HCl1reservoirpH6.0
28.6 mMMES-HCl1reservoirpH6.8
312 %(v/v)PEG4001reservoir
462 mM1reservoirMgCl2
514 mMdithiothreitol1reservoir
70.01 mMoligonucleotide1drop
80.9 mM1dropNaCl
91.4 mg/mlprotein1drop
6water1drop0.002ml
100.3 mMEDTA1drop
112.8 mMTris-HCl1droppH7.5
121.4 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: UNKNOWN
RadiationMonochromator: UNKNOWN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 21217 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.305 / % possible all: 86.8
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 94.7 % / Redundancy: 3 % / Num. measured all: 63314
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 86.8 % / Redundancy: 2.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: RECONSTITUTED HUMAN TOPOISOMERASE I COVALENT COMPLEX WITH 22 BASE PAIR DUPLEX DNA

Resolution: 2.8→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1445 7 %RANDOM
Rwork0.224 ---
obs0.224 21217 94.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.84 Å20 Å2-0.05 Å2
2--1.354 Å20 Å2
3---6.486 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 896 0 57 5285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.445 41 5.5 %
Rwork0.322 710 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51
LS refinement shell
*PLUS
% reflection Rfree: 5.5 %

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