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- PDB-6k8n: Crystal structure of the Sulfolobus solfataricus topoisomerase III -

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Basic information

Entry
Database: PDB / ID: 6k8n
TitleCrystal structure of the Sulfolobus solfataricus topoisomerase III
Componentstopoisomerase III
KeywordsISOMERASE / DNA BINDING PROTEIN / Topoisomerase III / type IA topoisomerase
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA recombination / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA topoisomerase I, archeal-type / DNA topoisomerase 3-like, TOPRIM domain / 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 I, archeal-type / DNA topoisomerase 3-like, TOPRIM domain / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, H.Q. / Zhang, J.H. / Zheng, X. / Zheng, Z.F. / Dong, Y.H. / Huang, L. / Gong, Y.
CitationJournal: To Be Published
Title: Crystal structures of the Sulfolobus solfataricus topoisomerase III reveal that its C-terminal novel zinc finger part is a unique decatenation domain
Authors: Wang, H.Q. / Zhang, J.H. / Zheng, X. / Zheng, Z.F. / Dong, Y.H. / Huang, L. / Gong, Y.
History
DepositionJun 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: topoisomerase III
B: topoisomerase III
C: topoisomerase III
D: topoisomerase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,9718
Polymers306,7094
Non-polymers2624
Water18,3751020
1
A: topoisomerase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7432
Polymers76,6771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: topoisomerase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7432
Polymers76,6771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: topoisomerase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7432
Polymers76,6771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: topoisomerase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7432
Polymers76,6771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.671, 90.040, 156.184
Angle α, β, γ (deg.)90.00, 100.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
topoisomerase III / DNA topoisomerase I family A (TopA)


Mass: 76677.344 Da / Num. of mol.: 4 / Mutation: Y318F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZJ8, EC: 5.99.1.2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 8% (v/v) Tacsimate (pH 4.4), and 13.75% (w/v) Polyethyleneglycerol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 172718 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 35.63 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2 / Num. unique obs: 8284 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAJ

2gaj


Resolution: 2.1→50 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.85
RfactorNum. reflection% reflection
Rfree0.2469 8481 4.94 %
Rwork0.2028 --
obs0.205 171737 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21559 0 4 1020 22583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821983
X-RAY DIFFRACTIONf_angle_d0.88529624
X-RAY DIFFRACTIONf_dihedral_angle_d14.5148430
X-RAY DIFFRACTIONf_chiral_restr0.0553354
X-RAY DIFFRACTIONf_plane_restr0.0063651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12380.33592650.28635188X-RAY DIFFRACTION94
2.1238-2.14880.33822630.27285240X-RAY DIFFRACTION94
2.1488-2.1750.32682410.26135259X-RAY DIFFRACTION94
2.175-2.20250.31892760.25615251X-RAY DIFFRACTION94
2.2025-2.23150.27912420.25335304X-RAY DIFFRACTION95
2.2315-2.26210.3013300.24795258X-RAY DIFFRACTION95
2.2621-2.29440.2933030.2415238X-RAY DIFFRACTION95
2.2944-2.32860.30512740.23315315X-RAY DIFFRACTION96
2.3286-2.3650.28243020.23315362X-RAY DIFFRACTION96
2.365-2.40380.28442720.24235317X-RAY DIFFRACTION96
2.4038-2.44520.31162670.245366X-RAY DIFFRACTION97
2.4452-2.48970.27852940.23355393X-RAY DIFFRACTION97
2.4897-2.53760.29422690.22815451X-RAY DIFFRACTION98
2.5376-2.58930.30152660.22535458X-RAY DIFFRACTION98
2.5893-2.64560.24272860.21375534X-RAY DIFFRACTION99
2.6456-2.70710.27312790.21415443X-RAY DIFFRACTION98
2.7071-2.77480.26982810.2215489X-RAY DIFFRACTION99
2.7748-2.84980.26352980.21745508X-RAY DIFFRACTION99
2.8498-2.93370.26172960.21995469X-RAY DIFFRACTION99
2.9337-3.02830.26972630.21355528X-RAY DIFFRACTION99
3.0283-3.13650.29662600.21445542X-RAY DIFFRACTION99
3.1365-3.2620.25873000.21345578X-RAY DIFFRACTION99
3.262-3.41040.2512950.20935537X-RAY DIFFRACTION99
3.4104-3.590.24373100.19845560X-RAY DIFFRACTION100
3.59-3.81480.22332890.1845565X-RAY DIFFRACTION100
3.8148-4.1090.22092840.17545649X-RAY DIFFRACTION100
4.109-4.52180.20262750.16775594X-RAY DIFFRACTION100
4.5218-5.17470.1982910.16435619X-RAY DIFFRACTION100
5.1747-6.5140.24152830.19485667X-RAY DIFFRACTION100
6.514-37.48870.19353270.17635574X-RAY DIFFRACTION98

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