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- PDB-7fvt: Crystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4... -

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Basic information

Entry
Database: PDB / ID: 7fvt
TitleCrystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1H-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4H-pyrido[3,2-b][1,4]oxazin-3-one
Components
  • DNA (5'-D(*AP*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 A Chimera
KeywordsISOMERASE / DNA GYRASE / TOPOISOMERASE
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
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 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
Similarity search - Domain/homology
Chem-6I0 / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.081 Å
AuthorsXu, B. / Benz, J. / Cumming, J.G. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens.
Authors: Cumming, J.G. / Kreis, L. / Kuhne, H. / Wermuth, R. / Vercruysse, M. / Kramer, C. / Rudolph, M.G. / Xu, Z.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)169,20411
Polymers168,4904
Non-polymers7147
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-106 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.938, 92.938, 407.651
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 / DNA chain , 2 types, 4 molecules ABCD

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


Mass: 78109.000 Da / Num. of mol.: 2 / Mutation: Y123F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: gyrB, SA0005, gyrA, SA0006 / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P66937, UniProt: Q99XG5, DNA topoisomerase (ATP-hydrolysing)
#2: DNA chain DNA (5'-D(*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)

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Non-polymers , 4 types, 552 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-6I0 / 6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one


Mass: 442.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: microbatch under paraffin oil: 500 nL each of ternary complex and reservoir consisting of 14% PEG5000 MME, 100mM BisTris/HCl pH 5.5: ternary complex made by mixing 14.5mg/mL gyrase in 20mM ...Details: microbatch under paraffin oil: 500 nL each of ternary complex and reservoir consisting of 14% PEG5000 MME, 100mM BisTris/HCl pH 5.5: ternary complex made by mixing 14.5mg/mL gyrase in 20mM HEPES/NaOH, pH7.0, 100mM Na2SO4, 3mM MnCl2, 0.5mM TCEP with twice the molar ratio of DNA duplex (5-AGCCGTAGGGCCCTACGGCT-3, 3-TCGGCATCCCGGGATGCCGA-5) and six times molar ratio of small molecule inhibitor.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.08→80.49 Å / Num. obs: 118711 / % possible obs: 100 % / Redundancy: 10.451 % / Biso Wilson estimate: 33.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.214 / Χ2: 0.812 / Net I/σ(I): 9.48 / Num. measured all: 1240593 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.08-2.1310.7673.1810.994236875587520.2013.34100
2.13-2.1910.6852.5341.1791540856885670.282.661100
2.19-2.2610.5771.9941.5488245834383430.4182.095100
2.26-2.3310.2251.6731.9582714809080890.5231.761100
2.33-2.410.1471.3412.4978947778177800.6141.412100
2.4-2.4910.8011.1533.1281859757975790.7781.211100
2.49-2.5810.6980.9743.8778740736073600.8291.024100
2.58-2.6910.5210.7365.173581699569940.8860.774100
2.69-2.810.2730.5616.4769428675867580.9290.591100
2.8-2.949.9050.4178.1863749643664360.9570.44100
2.94-3.110.7810.30710.8366487616961670.9820.322100
3.1-3.2910.7060.2213.8361870578057790.9880.231100
3.29-3.5210.4520.15617.4356872544154410.9910.164100
3.52-3.89.7020.12220.3249296508150810.9920.129100
3.8-4.1610.5160.09624.5149133467346720.9950.1100
4.16-4.6510.4950.08227.1444729426242620.9960.086100
4.65-5.3710.1040.08226.8437537371537150.9960.087100
5.37-6.5810.4140.08425.9832836315331530.9960.088100
6.58-9.310.5190.06630.6825761245124490.9970.0799.9
9.3-63.1649.770.05333.0713033133513340.9990.05699.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.12rc1_2801refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.081→63.164 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.88 / Stereochemistry target values: ML
Details: ligand not well defined by electron density. Chiral centers were assigned based on best geometry. Linker is disordered. Tried to use CSD-compatible conformation.
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 5184 5.04 %RANDOM
Rwork0.1996 97737 --
obs0.2022 102921 86.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.3 Å2 / Biso mean: 42.1545 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 2.081→63.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10632 798 37 545 12012
Biso mean--68.04 43.01 -
Num. residues----1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911744
X-RAY DIFFRACTIONf_angle_d0.88715979
X-RAY DIFFRACTIONf_chiral_restr0.051795
X-RAY DIFFRACTIONf_plane_restr0.0051965
X-RAY DIFFRACTIONf_dihedral_angle_d19.4577120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0808-2.10450.369450.2842961013
2.1045-2.12920.3059190.30563303499
2.1292-2.15520.3402600.31011138119830
2.1552-2.18250.33411060.3051941204752
2.1825-2.21120.33071250.28312604272969
2.2112-2.24150.35741270.2872817294475
2.2415-2.27350.34271500.27763146329683
2.2735-2.30740.34261530.2633356350990
2.3074-2.34350.32951910.25683573376495
2.3435-2.38190.33351920.2563720391299
2.3819-2.4230.31382230.240336713894100
2.423-2.46710.30071900.229937923982100
2.4671-2.51450.32421860.225438164002100
2.5145-2.56580.31442320.216336753907100
2.5658-2.62160.26381720.216637433915100
2.6216-2.68260.27642130.212537773990100
2.6826-2.74970.26262290.210237033932100
2.7497-2.82410.26761550.21138313986100
2.8241-2.90720.2662070.212237333940100
2.9072-3.0010.27242110.202437423953100
3.001-3.10820.24711770.198137893966100
3.1082-3.23270.24211930.197837133906100
3.2327-3.37980.24771980.193137743972100
3.3798-3.5580.22252190.182437443963100
3.558-3.78090.24072110.179837373948100
3.7809-4.07280.21262240.17437293953100
4.0728-4.48250.21292360.165737383974100
4.4825-5.13090.21991830.167137773960100
5.1309-6.46340.23882080.201137433951100
6.4634-63.19290.19791890.190537893978100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0797-0.1903-1.3280.96310.07651.80990.19810.58030.3926-0.207-0.0472-0.017-0.2724-0.1593-0.13240.35360.0553-0.01020.36840.06240.266787.663552.6897-49.5525
20.57890.22620.10330.46540.35121.3802-0.00060.0175-0.0791-0.07890.0083-0.0591-0.03450.1069-0.00870.29620.02840.0140.2120.02010.300476.595140.0731-16.0652
30.3832-0.5544-0.12831.2980.34730.5059-0.01650.0324-0.1163-0.0102-0.00670.15180.0611-0.02690.01640.2749-0.0160.01070.2169-0.0050.285674.605916.9324-18.6648
42.27440.4339-0.74741.8063-0.17191.44390.1327-0.3390.21680.28210.00810.0579-0.14910.0556-0.12730.28150.0115-0.00530.2663-0.06180.2046111.463452.3878-3.3271
50.70690.0404-0.180.59-0.23891.7352-0.03510.0519-0.08470.06840.04580.0104-0.1408-0.133-0.01510.2360.01640.00090.186-0.0650.2594121.504538.0095-37.151
60.90961.4269-0.4192.6642-0.98740.4958-0.0593-0.0301-0.1418-0.01480.0822-0.20120.1501-0.0017-0.00260.36790.0536-0.00460.2422-0.03810.3067116.54750.7152-26.5872
73.25783.6342-1.96184.0565-2.2051.2188-0.03960.18310.6281-1.3190.33690.7747-0.20.1033-0.25260.4388-0.0339-0.03380.2342-0.01880.3372120.876952.5908-30.1773
81.53282.225-0.74293.3107-0.78566.3357-0.03670.08090.2715-0.28780.2262-0.14640.1369-0.4835-0.19590.2671-0.01190.01870.2077-0.00830.2437108.563746.0373-20.2907
91.6404-0.365-1.25873.61540.01262.0872-0.3391-0.37640.1140.29810.1301-0.16810.27540.3080.21540.42250.1097-0.02730.31060.00310.289780.308155.3332-28.5359
104.9158-0.9911-1.31072.22460.60554.43610.0171-0.19050.73270.25180.26780.1361-0.35870.1877-0.23760.37650.1002-0.01580.3276-0.03640.365984.152351.6735-27.9247
115.3880.2793-1.91394.2424-0.06883.0286-0.19630.45770.1397-0.36840.2934-0.03730.2981-0.1886-0.06420.3641-0.0612-0.02220.2415-0.04440.303118.008752.3057-23.9709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 417 through 1032 )A417 - 1032
2X-RAY DIFFRACTION2chain 'A' and (resid 1033 through 1294 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1295 through 1490 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 417 through 1032 )B417 - 1032
5X-RAY DIFFRACTION5chain 'B' and (resid 1033 through 1347 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1348 through 1491 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )C1 - 5
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 10 )C6 - 10
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 20 )C11 - 20
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 10 )D1 - 10
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 20 )D11 - 20

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