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- PDB-6fm4: The crystal structure of S. aureus Gyrase complex with ID-130 and DNA -

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Basic information

Entry
Database: PDB / ID: 6fm4
TitleThe crystal structure of S. aureus Gyrase complex with ID-130 and DNA
Components
  • DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3')
  • DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
KeywordsISOMERASE / NBTIs / BACTERIAL TOPOISOMERASE / GYRASE
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
5'-O-CARBOXY-2'-DEOXYADENOSINE / Chem-DU5 / : / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOmbrato, R. / Garofalo, B. / Mangano, G. / Mancini, F.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens.
Authors: Magaro, G. / Prati, F. / Garofalo, B. / Corso, G. / Furlotti, G. / Apicella, C. / Mangano, G. / D'Atanasio, N. / Robinson, D. / Di Giorgio, F.P. / Ombrato, R.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.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,DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
E: DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,68910
Polymers167,5594
Non-polymers1,1306
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-87 kcal/mol
Surface area56920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.951, 92.951, 407.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules BD

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


Mass: 78109.000 Da / Num. of mol.: 2 / Mutation: Y1123F
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS GYRB (640) FUSED TO N-TERMINUS GYRA (1010). DOMAIN 544-579 DELETED AND REPLACED WITH TWO RESIDUES TG.
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Gene: gyrB, SA0005, gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3

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DNA chain , 2 types, 2 molecules EF

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


Mass: 5822.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3')


Mass: 5518.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 68 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-5UA / 5'-O-CARBOXY-2'-DEOXYADENOSINE


Type: DNA linking / Mass: 295.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N5O5
#6: Chemical ChemComp-DU5 / ~{N}-[3-(4-isoquinolin-1-ylpiperazin-1-yl)propyl]benzamide


Mass: 374.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N4O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 18% PEG 5000 MME, 0.1 M BISTRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→43.05 Å / Num. obs: 51255 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 30.68
Reflection shellResolution: 2.7→2.77 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.7→43.05 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.794 / SU B: 15.544 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 0.911 / ESU R Free: 0.391
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 2750 5.1 %RANDOM
Rwork0.2245 ---
obs0.2284 51255 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.83 Å2 / Biso mean: 39.691 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.8 Å2-0 Å2
2---0.8 Å2-0 Å2
3---2.58 Å2
Refinement stepCycle: final / Resolution: 2.7→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10606 758 56 62 11482
Biso mean--59.05 29.71 -
Num. residues----1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911668
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210993
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.91515885
X-RAY DIFFRACTIONr_angle_other_deg0.9713.00225231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84451338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12923.67534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.439152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9815118
X-RAY DIFFRACTIONr_chiral_restr0.0820.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022656
LS refinement shellResolution: 2.702→2.772 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 201 -
Rwork0.252 3767 -
all-3968 -
obs--99.25 %

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