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- PDB-2b9s: Crystal Structure of heterodimeric L. donovani topoisomerase I-va... -

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Basic information

Entry
Database: PDB / ID: 2b9s
TitleCrystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex
Components
  • 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*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
  • 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
  • DNA topoisomerase I-like protein
  • topoisomerase I-like protein
KeywordsISOMERASE/DNA / topoisomerase I / vanadate complex / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding
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) / 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 / Beta Complex / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / : / : / DNA / DNA (> 10) / DNA topoisomerase I-like protein / DNA topoisomerase I
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDavies, D.R. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA.
Authors: Davies, D.R. / Mushtaq, A. / Interthal, H. / Champoux, J.J. / Hol, W.G.
History
DepositionOct 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,6076
Polymers71,4925
Non-polymers1151
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.433, 106.102, 126.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterodimer consisting of one copy each of the large and small subunits and a DNA duplex.

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Components

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DNA chain , 3 types, 3 molecules CDE

#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(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'


Mass: 3684.453 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*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'


Mass: 6705.373 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 2 molecules AB

#4: Protein topoisomerase I-like protein


Mass: 50903.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: topoisomerase I, large subunit (LdTOP1L) / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: GenBank: 5305782, UniProt: Q9GPZ9*PLUS, DNA topoisomerase
#5: Protein DNA topoisomerase I-like protein


Mass: 7138.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: topoisomerase I, small subunit (LdTOP1S) / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: GenBank: 17528932, UniProt: Q8WQM6*PLUS, DNA topoisomerase

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Non-polymers , 2 types, 131 molecules

#6: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: 18% PEG 3350, 0.2 M Na2HPO4, 0.1 M LiCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Na2HPO411
3LiCl11
4H2O11
5PEG 335012
6Na2HPO412
7LiCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 43803 / Num. obs: 43803 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Χ2: 0.953
Reflection shellResolution: 2.27→2.35 Å / % possible obs: 71.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.408 / Num. measured obs: 3207 / Χ2: 0.812 / % possible all: 73

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
Blu-Icedata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→43.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.412 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2217 5.1 %RANDOM
Rwork0.231 ---
all0.233 43803 --
obs0.233 43746 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.498 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--0.5 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.27→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 889 3 130 4737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224813
X-RAY DIFFRACTIONr_angle_refined_deg1.5972.1726725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72623.523176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23415577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0151524
X-RAY DIFFRACTIONr_chiral_restr0.0950.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023414
X-RAY DIFFRACTIONr_nbd_refined0.1910.21869
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2213
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.21
X-RAY DIFFRACTIONr_mcbond_it1.49132452
X-RAY DIFFRACTIONr_mcangle_it2.3243810
X-RAY DIFFRACTIONr_scbond_it1.85132957
X-RAY DIFFRACTIONr_scangle_it2.78842915
LS refinement shellResolution: 2.273→2.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 126 -
Rwork0.337 2131 -
obs--100 %

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