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- PDB-3m7g: Structure of topoisomerase domain of topoisomerase V protein -

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Basic information

Entry
Database: PDB / ID: 3m7g
TitleStructure of topoisomerase domain of topoisomerase V protein
ComponentsTopoisomerase V
KeywordsISOMERASE / topoisomerase V / type IC topoisomerase / minimal catalytic fragment of topoisomerase V
Function / homology
Function and homology information


isomerase activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1010 / MutS, DNA mismatch repair protein, domain I - #50 / : / Topoisomerase V, second (HhH)2 tandem domain / DNA topoisomerase V, catalytic domain superfamily / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / MutS, DNA mismatch repair protein, domain I / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...Helicase, Ruva Protein; domain 3 - #1010 / MutS, DNA mismatch repair protein, domain I - #50 / : / Topoisomerase V, second (HhH)2 tandem domain / DNA topoisomerase V, catalytic domain superfamily / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / MutS, DNA mismatch repair protein, domain I / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRajan, R. / Taneja, B. / Mondragon, A.
CitationJournal: Structure / Year: 2010
Title: Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding.
Authors: Rajan, R. / Taneja, B. / Mondragon, A.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Topoisomerase V


Theoretical massNumber of molelcules
Total (without water)31,4681
Polymers31,4681
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)106.717, 119.390, 63.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Topoisomerase V


Mass: 31468.398 Da / Num. of mol.: 1 / Fragment: N-terminal 31kDa fragment (Topo-31)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / Gene: MK1436, top5, Topoisomerase V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q977W1
#2: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Sodium citrate pH 5.5, 23% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→79.79 Å / Num. all: 16304 / Num. obs: 16259 / % possible obs: 94.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.117 / Rsym value: 0.108 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.637 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Topoisomerase domain of topo-61 strcture (2CSB)

2csb


Resolution: 2.4→79.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 16.113 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24772 821 5.1 %RANDOM
Rwork0.20004 ---
obs0.2025 15419 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.261 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2---2.25 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 29 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222244
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.983036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25922.984124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63415404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21531
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8151.51381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04422163
X-RAY DIFFRACTIONr_scbond_it3.5973987
X-RAY DIFFRACTIONr_scangle_it5.4614.5873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 55 -
Rwork0.243 1136 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 37.064 Å / Origin y: 17.254 Å / Origin z: 1.377 Å
111213212223313233
T0.0966 Å20.003 Å2-0.0034 Å2--0.0086 Å20.0026 Å2---0.0394 Å2
L0.0044 °20.0241 °20.004 °2-0.2756 °20.1567 °2--0.1301 °2
S0.0439 Å °0.007 Å °0.0258 Å °0 Å °-0.0271 Å °-0.0188 Å °0.0164 Å °-0.0009 Å °-0.0169 Å °

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