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- PDB-1ois: YEAST DNA TOPOISOMERASE I, N-TERMINAL FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1ois
TitleYEAST DNA TOPOISOMERASE I, N-TERMINAL FRAGMENT
ComponentsDNA TOPOISOMERASE ITopoisomerase
KeywordsDNA BINDING PROTEIN / ISOMERASE / TOPOISOMERASE / DNA-BINDING PROTEIN
Function / homology
Function and homology information


chromatin organization => GO:0006325 / regulation of mitotic recombination / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / SUMOylation of DNA replication proteins / rDNA heterochromatin formation / replication fork protection complex / mitotic chromosome condensation / nuclear migration / DNA strand elongation involved in DNA replication ...chromatin organization => GO:0006325 / regulation of mitotic recombination / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / SUMOylation of DNA replication proteins / rDNA heterochromatin formation / replication fork protection complex / mitotic chromosome condensation / nuclear migration / DNA strand elongation involved in DNA replication / rRNA transcription / DNA topological change / chromosome segregation / transcription elongation by RNA polymerase II / DNA replication / chromatin remodeling / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 ...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) / 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 / Beta Complex / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLue, N. / Sharma, A. / Mondragon, A. / Wang, J.C.
CitationJournal: Structure / Year: 1995
Title: A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications.
Authors: Lue, N. / Sharma, A. / Mondragon, A. / Wang, J.C.
History
DepositionSep 14, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)26,0861
Polymers26,0861
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.200, 53.070, 116.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA TOPOISOMERASE I / Topoisomerase


Mass: 26085.756 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 141 - 363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BCY123/PYT-N / Description: YEAST GALACTOSE INDUCIBLE EXPRESSION SYSTEM / Gene: TOP1 / Plasmid: PYT-N / Gene (production host): TOP1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04786, DNA topoisomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.8 Å3/Da / Density % sol: 52 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG33501reservoir
20.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionNum. obs: 24425 / % possible obs: 95.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 39 Å / Num. measured all: 127777
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.278

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.29 -
Rwork0.222 -
obs0.222 24425
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 0 225 2462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.73

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