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- PDB-5iwi: 1.98A structure of GSK945237 with S.aureus DNA gyrase and singly ... -

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Basic information

Entry
Database: PDB / ID: 5iwi
Title1.98A structure of GSK945237 with S.aureus DNA gyrase and singly nicked DNA
Components
  • (DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ...) x 2
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR / fusion protein
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / Histidine kinase/HSP90-like ATPase superfamily / 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-6EJ / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsBax, B.D. / Miles, T.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases.
Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Jones, G.E. / ...Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Jones, G.E. / Kusalakumari Sukmar, S.K. / Markwell, R.E. / Minthorn, E.A. / Rittenhouse, S. / Gwynn, M.N. / Pearson, N.D.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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_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.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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')
F: DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
G: DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,05222
Polymers168,4797
Non-polymers1,57315
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24790 Å2
ΔGint-132 kcal/mol
Surface area56130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.897, 92.897, 410.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 22605.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A /


Mass: 55521.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3

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DNA chain , 1 types, 1 molecules E

#3: DNA chain DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')


Mass: 6112.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHAIN E WAS A 20MER. CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT. NOTE THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER ...Details: CHAIN E WAS A 20MER. CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT. NOTE THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NON-CRYSTALLOGRAPHIC TWOFOLD AXIS.
Source: (synth.) synthetic construct (others)

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DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ... , 2 types, 2 molecules FG

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


Mass: 2473.626 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED ...Details: CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NC TWOFOLD AXIS.
Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED ...Details: CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NC TWOFOLD AXIS.
Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 965 molecules

#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-6EJ / (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one


Mass: 451.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FN5O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 11% PEG 3350, 170mM BisTris pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 137423 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/av σ(I): 14.2 / Net I/σ(I): 14.2
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.6 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2xcs

2xcs


Resolution: 1.98→18 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.895 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.20169 2759 2 %RANDOM
Rwork0.16552 ---
obs0.16625 134611 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å2-0 Å2
2---0.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.98→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10637 811 97 950 12495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01813625
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.86718782
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.05951514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07623.899595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.367152210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.04215130
X-RAY DIFFRACTIONr_chiral_restr0.0940.21993
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110035
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4464.5825858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.387.7057438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2064.8687767
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.51121.30421724
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 199 -
Rwork0.277 9674 -
obs--97.6 %

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