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- PDB-5bs8: Crystal structure of a topoisomerase II complex -

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Basic information

Entry
Database: PDB / ID: 5bs8
TitleCrystal structure of a topoisomerase II complex
Components
  • (DNA gyrase subunit ...) x 2
  • (DNA substrate 24-mer ...) x 2
KeywordsIsomerase/DNA / protein-DNA complex / topoisomerase II / Isomerase-DNA complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MFX / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsBlower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.
Authors: Blower, T.R. / Williamson, B.H. / Kerns, R.J. / Berger, J.M.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B
E: DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA
F: DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC
G: DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC
H: DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,33914
Polymers198,4398
Non-polymers9006
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.357, 83.070, 129.856
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe double-stranded DNAs are superposed copies of each other, overlaid in opposite orientations (because directionality could not be resolved). Therefore in reality, rather than in the model, the biological assembly would in fact be hexameric - four proteins and one double-stranded DNA.

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Components

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DNA gyrase subunit ... , 2 types, 4 molecules ACBD

#1: Protein DNA gyrase subunit A


Mass: 56209.422 Da / Num. of mol.: 2 / Fragment: GyrA tower and C-gate domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrA, Rv0006, MTCY10H4.04 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P9WG47, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B


Mass: 28272.412 Da / Num. of mol.: 2 / Fragment: GyrB toprim domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrB, Rv0005, MTCY10H4.03 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P9WG45, EC: 5.99.1.3

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DNA substrate 24-mer ... , 2 types, 4 molecules EHFG

#3: DNA chain DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA


Mass: 7417.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC


Mass: 7319.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 409 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MFX / 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid / moxifloxacin


Mass: 401.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24FN3O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.58 % / Description: Very thin planar crystals (<10 uM thick), up to 200 x 300 uM2 surface area
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris-HCl, 13-15% PEG 4000, 200 mM MgCl2, 6.25% PEG 400
PH range: 7.0 to 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2014
RadiationMonochromator: Si 220 filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.399→102.3 Å / Num. obs: 83492 / % possible obs: 97.68 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08799 / Net I/σ(I): 10.66
Reflection shellResolution: 2.399→2.485 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.99 / Rejects: 0 / % possible all: 93.22

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Processing

Software
NameClassification
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKK

2xkk


Resolution: 2.399→102.252 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 4167 4.99 %
Rwork0.1957 79313 -
obs0.1976 83480 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 319.72 Å2 / Biso mean: 77.0026 Å2 / Biso min: 27.31 Å2
Refinement stepCycle: final / Resolution: 2.399→102.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11538 1640 108 403 13689
Biso mean--53.71 54.67 -
Num. residues----1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413652
X-RAY DIFFRACTIONf_angle_d0.68618769
X-RAY DIFFRACTIONf_chiral_restr0.0312118
X-RAY DIFFRACTIONf_plane_restr0.0032179
X-RAY DIFFRACTIONf_dihedral_angle_d16.8535313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3991-2.42630.41851170.38372314243186
2.4263-2.45490.39171340.39082602273696
2.4549-2.48480.37061320.37192640277297
2.4848-2.51630.3821240.35692648277298
2.5163-2.54940.40791200.35022552267296
2.5494-2.58430.38281360.32682643277998
2.5843-2.62120.33131700.30272647281799
2.6212-2.66030.31011360.28492669280599
2.6603-2.70190.28021370.27032692282999
2.7019-2.74620.30531230.26842669279299
2.7462-2.79360.28551210.2662706282799
2.7936-2.84440.30861570.25162667282499
2.8444-2.89910.28451410.25012641278299
2.8991-2.95830.28151620.24312659282199
2.9583-3.02260.29931370.24532644278198
3.0226-3.09290.29121460.25192645279198
3.0929-3.17030.2611440.24762593273797
3.1703-3.2560.23011480.22292657280599
3.256-3.35180.27131380.21042684282299
3.3518-3.460.26741270.19562701282899
3.46-3.58370.2371540.18652642279699
3.5837-3.72720.21491290.1782692282198
3.7272-3.89680.20751420.16572640278298
3.8968-4.10220.22961440.15552551269595
4.1022-4.35930.16961580.142674283298
4.3593-4.69590.1571560.13232658281498
4.6959-5.16840.18011280.1342708283698
5.1684-5.91620.21311360.16732686282298
5.9162-7.45350.21731330.16862662279597
7.4535-102.34480.17061370.162727286496

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