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- PDB-4plb: Crystal Structure of S.A. gyrase-AM8191 complex -

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Basic information

Entry
Database: PDB / ID: 4plb
TitleCrystal Structure of S.A. gyrase-AM8191 complex
Components
  • Chimera protein of DNA gyrase subunits B and A
  • DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
KeywordsISOMERASE/ISOMERASE Inhibitor/DNA / gyase inhibitor complex / ISOMERASE-ISOMERASE Inhibitor-DNA complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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-31N / : / 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 / Resolution: 2.69 Å
AuthorsLu, J. / Patel, S. / Soisson, S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents.
Authors: Singh, S.B. / Kaelin, D.E. / Wu, J. / Miesel, L. / Tan, C.M. / Meinke, P.T. / Olsen, D. / Lagrutta, A. / Bradley, P. / Lu, J. / Patel, S. / Rickert, K.W. / Smith, R.F. / Soisson, S. / Wei, C. ...Authors: Singh, S.B. / Kaelin, D.E. / Wu, J. / Miesel, L. / Tan, C.M. / Meinke, P.T. / Olsen, D. / Lagrutta, A. / Bradley, P. / Lu, J. / Patel, S. / Rickert, K.W. / Smith, R.F. / Soisson, S. / Wei, C. / Fukuda, H. / Kishii, R. / Takei, M. / Fukuda, Y.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
B: Chimera protein of DNA gyrase subunits B and A
D: Chimera protein of DNA gyrase subunits B and A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,32910
Polymers168,4224
Non-polymers9086
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16230 Å2
ΔGint-111 kcal/mol
Surface area56470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.310, 93.310, 410.197
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 chain / Protein , 2 types, 4 molecules EFBD

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


Mass: 6135.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Chimera protein of DNA gyrase subunits B and A


Mass: 78074.922 Da / Num. of mol.: 2
Fragment: DNA gyrase subunit B (UNP P0A0K8 residues 410-543 and 580-644), DNA gyrase subunit A (UNP P20831 residues 2-491)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, gyrA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0K8, UniProt: P20831, EC: 5.99.1.3

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Non-polymers , 4 types, 79 molecules

#3: Chemical ChemComp-31N / 6-[({(1r,4S)-1-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-2-oxabicyclo[2.2.2]oct-4-yl}amino)methyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one


Mass: 509.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28FN5O5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15.33 % PEG MME 5K, 50 mM Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→410.2 Å / Num. obs: 55628 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 68.33 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.3
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.9.7 / Classification: refinement
RefinementResolution: 2.69→27.12 Å / Cor.coef. Fo:Fc: 0.9402 / Cor.coef. Fo:Fc free: 0.9166 / SU R Cruickshank DPI: 0.525 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.454 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2812 5.07 %RANDOM
Rwork0.1765 ---
obs0.1788 55447 99.62 %-
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.4436 Å20 Å20 Å2
2--2.4436 Å20 Å2
3----4.8871 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: 1 / Resolution: 2.69→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 800 54 73 11507
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111675HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2115927HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4425SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes311HARMONIC8
X-RAY DIFFRACTIONt_gen_planes1612HARMONIC8
X-RAY DIFFRACTIONt_it11675HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.94
X-RAY DIFFRACTIONt_other_torsion18.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1548SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13200SEMIHARMONIC4
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 210 5.42 %
Rwork0.205 3664 -
all0.2082 3874 -
obs--99.62 %

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