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- PDB-2o59: Structure of E. coli topoisomerase III in complex with an 8-base ... -

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Basic information

Entry
Database: PDB / ID: 2o59
TitleStructure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol pH 8.0
Components
  • 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
  • DNA topoisomerase 3
KeywordsISOMERASE/DNA / topoisomerase type IA complex with ssDNA / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding
Similarity search - Function
DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 ...DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / Topoisomerase I; domain 3 / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DNA / DNA topoisomerase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChangela, A. / DiGate, R.J. / Mondragon, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate.
Authors: Changela, A. / Digate, R.J. / Mondragon, A.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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(*CP*GP*CP*AP*AP*CP*TP*T)-3'
D: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
A: DNA topoisomerase 3
B: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2087
Polymers153,0774
Non-polymers1313
Water2,558142
1
C: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
A: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5743
Polymers76,5382
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'
B: DNA topoisomerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6344
Polymers76,5382
Non-polymers962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.590, 101.590, 453.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsComplex of E. coli topoisomerase III with DNA. Two molecules in the asymmetric unit. Each molecule in a different conformational state.

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Components

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


Mass: 2386.593 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA topoisomerase 3 / DNA topoisomerase III


Mass: 74151.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: topB / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P14294, EC: 5.99.1.2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)SO411
2Sodium citrate11
3NaCl11
4HOH11
5(NH4)SO412
6Sodium citrate12
7NaCl12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.503→29.534 Å / Num. obs: 81050 / % possible obs: 97.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.8 / Num. measured all: 15495 / Num. unique all: 5081 / Rsym value: 0.269 / % possible all: 88.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
XDSdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D6M, 1I7D

1d6m

1i7d


Resolution: 2.5→29.534 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.909 / SU B: 14.55 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4038 5 %RANDOM
Rwork0.221 ---
obs0.223 81032 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.73 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9909 296 2 146 10353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210459
X-RAY DIFFRACTIONr_angle_refined_deg1.241.99614235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4751239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70323.306490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.744151747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511597
X-RAY DIFFRACTIONr_chiral_restr0.0790.21577
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027898
X-RAY DIFFRACTIONr_nbd_refined0.2050.24354
X-RAY DIFFRACTIONr_nbtor_refined0.3030.26994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2346
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.210
X-RAY DIFFRACTIONr_mcbond_it0.5691.56429
X-RAY DIFFRACTIONr_mcangle_it0.977210061
X-RAY DIFFRACTIONr_scbond_it1.39634623
X-RAY DIFFRACTIONr_scangle_it2.3114.54174
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 216 -
Rwork0.309 5122 -
obs-5338 88 %

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