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- PDB-5gvc: Human Topoisomerase IIIb topo domain -

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Basic information

Entry
Database: PDB / ID: 5gvc
TitleHuman Topoisomerase IIIb topo domain
ComponentsDNA topoisomerase 3-beta-1
KeywordsISOMERASE / Topoisomerase
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / chromosome segregation / DNA recombination / DNA repair / DNA binding ...DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / chromosome segregation / DNA recombination / DNA repair / DNA binding / RNA binding / nucleus
Similarity search - Function
DNA topoisomerase 3-like, TOPRIM domain / 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. ...DNA topoisomerase 3-like, TOPRIM domain / 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. / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 3-beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.436 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Takahashi, T.S. / Fukai, S.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Authors: Goto-Ito, S. / Yamagata, A. / Takahashi, T.S. / Sato, Y. / Fukai, S.
History
DepositionSep 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 3-beta-1
B: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6854
Polymers138,6362
Non-polymers492
Water7,404411
1
A: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3422
Polymers69,3181
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area29000 Å2
MethodPISA
2
B: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3422
Polymers69,3181
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.088, 93.665, 91.608
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA topoisomerase 3-beta-1 / DNA topoisomerase III beta-1


Mass: 69318.133 Da / Num. of mol.: 2 / Fragment: UNP residues 1-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP3B, TOP3B1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95985, DNA topoisomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-Na, 0.2 M MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 55090 / % possible obs: 99.1 % / Redundancy: 6.7 % / Net I/σ(I): 13.4
Reflection shellResolution: 2.44→2.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CGY

4cgy


Resolution: 2.436→49.718 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 2793 5.07 %
Rwork0.182 --
obs0.1844 55088 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.436→49.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9591 0 2 411 10004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029800
X-RAY DIFFRACTIONf_angle_d0.68513254
X-RAY DIFFRACTIONf_dihedral_angle_d12.5943669
X-RAY DIFFRACTIONf_chiral_restr0.0251467
X-RAY DIFFRACTIONf_plane_restr0.0031714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4357-2.47770.29681360.23912406X-RAY DIFFRACTION91
2.4777-2.52270.31891320.24342617X-RAY DIFFRACTION100
2.5227-2.57120.30221420.23332635X-RAY DIFFRACTION100
2.5712-2.62370.28711280.22522629X-RAY DIFFRACTION99
2.6237-2.68080.27081500.21782631X-RAY DIFFRACTION99
2.6808-2.74310.28251280.20992594X-RAY DIFFRACTION99
2.7431-2.81170.26881330.21792595X-RAY DIFFRACTION99
2.8117-2.88770.24991310.2172592X-RAY DIFFRACTION98
2.8877-2.97270.26431550.22052629X-RAY DIFFRACTION100
2.9727-3.06860.28621390.2252625X-RAY DIFFRACTION100
3.0686-3.17830.32171590.22752609X-RAY DIFFRACTION99
3.1783-3.30550.26031400.21662616X-RAY DIFFRACTION99
3.3055-3.45590.27011500.1982605X-RAY DIFFRACTION99
3.4559-3.63810.20491380.17952593X-RAY DIFFRACTION98
3.6381-3.86590.22191320.16822645X-RAY DIFFRACTION100
3.8659-4.16430.19911450.15452661X-RAY DIFFRACTION99
4.1643-4.58310.16711320.1362617X-RAY DIFFRACTION99
4.5831-5.24560.191550.14462629X-RAY DIFFRACTION99
5.2456-6.60650.20451400.15862660X-RAY DIFFRACTION99
6.6065-49.72820.14171280.13752707X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.4613 Å / Origin y: 17.4944 Å / Origin z: -15.61 Å
111213212223313233
T0.224 Å2-0.0133 Å2-0.0009 Å2-0.262 Å2-0.0028 Å2--0.2819 Å2
L0.0532 °2-0.1396 °20.0618 °2-0.3285 °2-0.1926 °2--0.2219 °2
S0.0207 Å °0.0168 Å °-0.015 Å °0.0001 Å °-0.0081 Å °0.0856 Å °0.0079 Å °-0.0227 Å °-0.0105 Å °
Refinement TLS groupSelection details: all

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