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- PDB-7lhz: K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA an... -

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Basic information

Entry
Database: PDB / ID: 7lhz
TitleK. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid (compound 25)
Components
  • DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
  • DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimeraTopoisomerase
KeywordsISOMERASE/DNA/INHIBITOR / Gyrase / DNA topoisomerase / ParC / ParE / ISOMERASE-DNA-INHIBITOR complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase IV, subunit B, Gram-negative / 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 ...DNA topoisomerase IV, subunit B, Gram-negative / 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-Y21 / DNA / DNA (> 10) / DNA topoisomerase 4 subunit B / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae 342 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsNoeske, J. / Shu, W. / Bellamacina, C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria.
Authors: Lapointe, G. / Skepper, C.K. / Holder, L.M. / Armstrong, D. / Bellamacina, C. / Blais, J. / Bussiere, D. / Bian, J. / Cepura, C. / Chan, H. / Dean, C.R. / De Pascale, G. / Dhumale, B. / ...Authors: Lapointe, G. / Skepper, C.K. / Holder, L.M. / Armstrong, D. / Bellamacina, C. / Blais, J. / Bussiere, D. / Bian, J. / Cepura, C. / Chan, H. / Dean, C.R. / De Pascale, G. / Dhumale, B. / Fisher, L.M. / Fulsunder, M. / Kantariya, B. / Kim, J. / King, S. / Kossy, L. / Kulkarni, U. / Lakshman, J. / Leeds, J.A. / Ling, X. / Lvov, A. / Ma, S. / Malekar, S. / McKenney, D. / Mergo, W. / Metzger, L. / Mhaske, K. / Moser, H.E. / Mostafavi, M. / Namballa, S. / Noeske, J. / Osborne, C. / Patel, A. / Patel, D. / Patel, T. / Piechon, P. / Polyakov, V. / Prajapati, K. / Prosen, K.R. / Reck, F. / Richie, D.L. / Sanderson, M.R. / Satasia, S. / Savani, B. / Selvarajah, J. / Sethuraman, V. / Shu, W. / Tashiro, K. / Thompson, K.V. / Vaarla, K. / Vala, L. / Veselkov, D.A. / Vo, J. / Vora, B. / Wagner, T. / Wedel, L. / Williams, S.L. / Yendluri, S. / Yue, Q. / Yifru, A. / Zhang, Y. / Rivkin, A.
History
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
D: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
A: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
B: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
P: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
K: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
I: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
J: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
G: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
H: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
F: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,44222
Polymers368,55912
Non-polymers1,88310
Water724
1
A: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
B: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
G: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
H: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
F: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,22111
Polymers184,2796
Non-polymers9425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-85 kcal/mol
Surface area62330 Å2
MethodPISA
2
C: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
D: DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera
P: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
K: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
I: DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')
J: DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,22111
Polymers184,2796
Non-polymers9425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13920 Å2
ΔGint-102 kcal/mol
Surface area65110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.185, 159.818, 144.059
Angle α, β, γ (deg.)90.000, 94.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules CDAB

#1: Protein
DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera / Topoisomerase / Topoisomerase IV subunit B / Topoisomerase IV subunit A


Mass: 84199.500 Da / Num. of mol.: 4
Fragment: UNP residues 390-631 (parE) + UNP residues 1-490 (parC)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae 342 (bacteria) / Strain: 342 / Gene: parE, NCTC5052_03997, parC, SAMEA4873570_03328 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A377Y395, UniProt: A0A486EJ79, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 2 types, 8 molecules PJHEKIGF

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


Mass: 3354.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae 342 (bacteria)
#3: DNA chain
DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')


Mass: 4586.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae 342 (bacteria)

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Non-polymers , 4 types, 14 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-Y21 / (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid


Mass: 387.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C20H22FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 20% MPD, 10 mM magnesium chloride, 0.5 mM spermine, 100 mM sodium cacodylate, pH 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→54.91 Å / Num. obs: 63836 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.247 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
3.3-3.353.21.7680.530460.31295.3
8.94-54.913.50.06411.532830.992100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EIX

5eix


Resolution: 3.3→46.92 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3083 3287 5.17 %
Rwork0.2826 60317 -
obs0.2839 63604 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.3 Å2 / Biso mean: 83.2138 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 3.3→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19019 1870 160 4 21053
Biso mean--75.57 56.21 -
Num. residues----2820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.350.44921650.37932463262895
3.35-3.40.38951250.37132603272899
3.4-3.460.37231520.366426272779100
3.46-3.520.40911310.36412635276699
3.52-3.580.37171420.348726222764100
3.58-3.650.30441300.32142647277799
3.65-3.720.34031360.322225952731100
3.72-3.80.37241500.317726422792100
3.8-3.890.32581340.303426012735100
3.89-3.990.31831610.296426192780100
3.99-4.10.33171570.297626182775100
4.1-4.220.30381730.285925872760100
4.22-4.350.29491590.282225942753100
4.35-4.510.26641590.267926232782100
4.51-4.690.28931440.255926282772100
4.69-4.90.24041310.254126272758100
4.9-5.160.31071450.272626512796100
5.16-5.480.31431130.281926562769100
5.48-5.910.28051210.292726672788100
5.91-6.50.36571390.294626342773100
6.5-7.440.31631570.297326342791100
7.44-9.360.28091380.224226652803100
9.36-46.920.24061250.22592679280498
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)
11.99090.14820.3880.3440.67183.14590.2728-1.034-1.19210.92330.1594-1.19530.8094-0.0331-0.39741.0713-0.0461-0.62270.78590.13481.5265146.1108-46.0591151.3759
24.79612.64240.34054.0576-1.4380.999-0.87481.1240.5897-0.25510.6191-0.2802-0.09890.43830.34460.8167-0.104-0.1650.80340.0240.7389121.1564-51.202137.2359
31.4061-1.0436-1.42171.3583-0.62554.98710.27580.7328-0.2465-0.29220.45660.04231.0456-0.3469-0.72030.7074-0.0415-0.39720.7395-0.15711.5463145.5521-47.7021134.948
42.82460.55740.85992.7886-0.54.292-0.0382-0.0514-0.2173-0.19850.29720.0980.0497-0.1415-0.25210.3416-0.0016-0.08430.4801-0.11730.4927133.0316-17.5994128.8517
52.48872.67251.42986.1833.36343.73520.05950.49210.0130.88720.3178-0.01250.30680.4655-0.36510.4618-0.0317-0.01190.491-0.09570.5526150.8366-0.5526139.8792
68.66361.96592.94470.78220.79751.6349-0.37991.0357-0.277-0.13880.3823-0.074-0.30250.3209-0.00780.7587-0.1197-0.24890.55550.07890.5467108.5523-19.9589109.0881
71.75941.7511-0.55594.6905-0.67914.75780.6978-1.53960.77980.753-0.3872-0.1368-0.29740.0332-0.32220.7193-0.19510.03771.3401-0.26340.7683122.4644-4.3641169.014
82.25670.9233-0.80321.8465-0.09143.81730.0918-1.2358-0.30950.151-0.1778-0.15510.52910.00020.08550.5892-0.1532-0.13851.06150.31630.6512105.2679-34.0362159.6627
91.51660.49220.07481.0231-0.42292.67850.1224-0.9032-0.46940.2486-0.1907-0.22320.47-0.07170.00640.6692-0.0028-0.12520.86310.3170.63594.7794-37.3787152.9539
103.14590.05110.80652.605-1.43062.0836-0.23690.66020.5193-1.0772-0.05220.4715-1.0185-1.05920.21111.40040.1838-0.23660.82750.02860.611888.4862-37.350152.9877
112.6231-0.5394-2.21111.22811.27782.2397-0.315-0.00520.5372-0.37020.3651-0.1964-0.6563-0.0048-0.07121.43940.0747-0.0530.6120.01840.645196.4299-34.334369.5397
122.38280.0771-0.1481.7653-0.71893.8391-0.1605-0.07680.09680.20390.37640.0973-0.5522-0.6203-0.22270.53480.0612-0.01910.4892-0.03490.348699.4387-62.740977.0405
133.17612.89212.87615.39175.10327.43850.30430.1195-0.4610.07320.1295-0.35040.420.2637-0.43610.43580.0439-0.07220.4244-0.07270.4381108.168-79.998158.8393
141.3349-0.0601-1.79630.160.94718.25080.2141-0.168-0.1118-0.01250.0456-0.0031-0.54790.2732-0.31710.69240.1187-0.1230.40430.00530.4667107.4297-63.1206106.6699
153.5472-0.1402-0.2721.77830.39893.2635-0.50390.4845-0.2212-0.1678-0.01260.15860.0777-0.87950.50240.67710.0985-0.03971.0691-0.03660.643962.2798-64.296873.3644
161.49520.18171.01250.41220.04651.6399-0.2230.12360.3241-0.1158-0.13750.2164-0.5709-0.90690.41950.86940.4546-0.15321.235-0.04670.797262.7418-50.8155102.3269
176.77562.6976-5.80870.9774-2.28674.9625-0.5457-2.5506-0.1911-0.18030.1272-0.9145-0.28611.13340.43840.6576-0.0491-0.30360.766-0.09630.9373148.5314-22.3512141.5119
183.6589-2.5791-5.02164.20943.39217.8330.2892-1.9404-0.66251.1356-0.0329-0.53711.4273-0.0072-0.23461.1005-0.4962-0.35971.96440.21691.0012122.9671-28.9709174.3324
193.19750.6673-2.03540.1992-0.56931.76820.4553-0.1717-0.00260.3182-0.3156-0.0266-1.03140.0724-0.15760.6886-0.0507-0.2140.6323-0.21540.8799147.6688-22.0195143.7547
200.2644-0.3559-0.46580.65330.77491.0676-0.3802-1.5077-0.10311.4561-0.0373-0.7957-0.13490.80650.25520.7265-0.5864-1.0712.86350.25310.2925120.0281-27.73175.1792
219.06192.1892.0842.0679-0.96621.84220.05940.2702-1.46890.0359-0.1127-0.31350.2579-0.41950.03851.0644-0.12450.12680.6357-0.07870.629196.3397-60.285556.4075
224.45061.07334.58854.66511.35329.7311-0.10462.6193-0.0184-1.66780.43280.3723-0.0709-0.1657-0.31461.0141-0.0386-0.05591.81590.08820.661558.9406-55.834165.6954
234.35314.0244-1.39136.16751.32353.3876-0.71460.93560.4473-0.73880.2610.6501-0.8463-1.87320.39070.95920.1539-0.15751.7943-0.13820.819659.8899-56.086562.6779
248.2873-0.72672.58238.2119-0.04150.79410.10752.1027-0.291-1.41620.4003-0.7244-0.4101-1.0437-0.53031.0288-0.0477-0.01620.8483-0.0150.51598.603-60.784357.0666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 400 through 523 )A400 - 523
2X-RAY DIFFRACTION2chain 'A' and (resid 524 through 571 )A524 - 571
3X-RAY DIFFRACTION3chain 'A' and (resid 572 through 1011 )A572 - 1011
4X-RAY DIFFRACTION4chain 'A' and (resid 1012 through 1242 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1243 through 1342 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1343 through 1484 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 399 through 1028 )B399 - 1028
8X-RAY DIFFRACTION8chain 'B' and (resid 1029 through 1234 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1235 through 1480 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 401 through 523 )C401 - 523
11X-RAY DIFFRACTION11chain 'C' and (resid 524 through 1009 )C524 - 1009
12X-RAY DIFFRACTION12chain 'C' and (resid 1010 through 1197 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1198 through 1342 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1343 through 1483 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 399 through 1234 )D399 - 1234
16X-RAY DIFFRACTION16chain 'D' and (resid 1235 through 1483 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 402 through 411 )E402 - 411
18X-RAY DIFFRACTION18chain 'F' and (resid 512 through 526 )F512 - 526
19X-RAY DIFFRACTION19chain 'G' and (resid 712 through 725 )G712 - 725
20X-RAY DIFFRACTION20chain 'H' and (resid 602 through 611 )H602 - 611
21X-RAY DIFFRACTION21chain 'I' and (resid 312 through 324 )I312 - 324
22X-RAY DIFFRACTION22chain 'J' and (resid 204 through 211 )J204 - 211
23X-RAY DIFFRACTION23chain 'K' and (resid 112 through 124 )K112 - 124
24X-RAY DIFFRACTION24chain 'P' and (resid 3 through 11 )P3 - 11

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