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- PDB-9nx4: Crystal Structure of a P. Aeruginosa Gyrase Chimera In Complex wi... -

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Basic information

Entry
Database: PDB / ID: 9nx4
TitleCrystal Structure of a P. Aeruginosa Gyrase Chimera In Complex with 20mer DNA and Ciprofloxacin
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
KeywordsDNA BINDING PROTEIN / Gyrase / Pseudomonas / DNA binding / Ciprofloxacin
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 / DNA gyrase subunit B, TOPRIM domain ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / 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 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
CITRIC ACID / Chem-CPF / : / DNA / DNA (> 10) / DNA gyrase subunit A / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPedersen, L.C. / Doetsch, P.W. / Garcia-Villada, L. / Degtyareva, N. / Perera, U.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZICES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZICES043010 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z1AES103328 United States
Citation
Journal: Biomolecules / Year: 2026
Title: Structural and Computational Analysis of Pseudomonas aeruginosa DNA Gyrase Reveals Molecular Characteristics That May Contribute to Ciprofloxacin Resistance.
Authors: Perera, L. / Garcia-Villada, L. / Kaminski, A.M. / Degtyareva, N. / Pedersen, L.C. / Doetsch, P.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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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
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,93613
Polymers111,5352
Non-polymers1,40011
Water28816
1
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')
hetero molecules

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')
hetero molecules

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')
hetero molecules

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')
hetero molecules

A: DNA gyrase subunit B,DNA gyrase subunit A
hetero molecules

A: DNA gyrase subunit B,DNA gyrase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,87732
Polymers235,3426
Non-polymers3,53426
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z2
Unit cell
Length a, b, c (Å)179.033, 179.033, 163.298
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

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


Mass: 105399.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSAAA(tag)-GyrB(residues 397-806)-GGS(linker)-GyrA(residues 2-525),GSAAA(tag)-GyrB(residues 397-806)-GSS(linker)-GyrA(residues 2-525)
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: gyrB, gyrA, CSB93_3133 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q9S1C7, UniProt: A0A2R3INH2, 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.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 6 types, 27 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CPF / 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID / ciprofloxacin


Mass: 331.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18FN3O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium citrate pH 6.0 14% PEG 4000 200mM Ammonium Sulfate 1mM MnCl2 1mM ciprofloxacin
Temp details: room termperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 36343 / % possible obs: 99.2 % / Redundancy: 15.5 % / Biso Wilson estimate: 51.72 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.043 / Rrim(I) all: 0.174 / Net I/σ(I): 3.7
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1785 / CC1/2: 0.815 / Rpim(I) all: 0.327 / Rrim(I) all: 1.296

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→43.67 Å / SU ML: 0.3688 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1800 4.99 %
Rwork0.205 34296 -
obs0.2065 36096 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.3 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 407 85 16 6182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786325
X-RAY DIFFRACTIONf_angle_d0.95448667
X-RAY DIFFRACTIONf_chiral_restr0.0524977
X-RAY DIFFRACTIONf_plane_restr0.00881061
X-RAY DIFFRACTIONf_dihedral_angle_d17.38592429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.32841370.31492573X-RAY DIFFRACTION98.55
2.92-3.010.32341350.28272591X-RAY DIFFRACTION99.09
3.01-3.110.29321350.26462589X-RAY DIFFRACTION98.55
3.11-3.220.30211360.25252566X-RAY DIFFRACTION97.44
3.22-3.350.30811330.23722611X-RAY DIFFRACTION99.2
3.35-3.50.2661410.23522615X-RAY DIFFRACTION98.96
3.5-3.680.26171370.19192633X-RAY DIFFRACTION99.21
3.68-3.920.261400.18432647X-RAY DIFFRACTION99.11
3.92-4.220.21561370.16922629X-RAY DIFFRACTION99.14
4.22-4.640.16471400.15092674X-RAY DIFFRACTION99.22
4.64-5.310.17511400.15442676X-RAY DIFFRACTION98.98
5.31-6.690.21471410.21632662X-RAY DIFFRACTION96.92
6.69-43.670.21271480.21492830X-RAY DIFFRACTION97.29
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)
11.097969069780.103477731260.5405048476381.288093507040.349206804351.49965160328-0.0372555549214-0.217958227709-0.09469248117070.3411198673380.0863706949193-0.1382943717470.04514917369350.0931000119893-1.53408209059E-90.5267776231190.0211981777858-0.01479814695760.514695465496-0.01823173984620.435162613535-43.979657544-11.300848151514.0829393786
21.25131298536-0.274537558206-0.01640959437030.697732627605-0.01666987042940.2654141313150.01147148344780.0112988315946-0.333900617708-0.1107593220920.008838847078410.1397777748620.0280729975672-0.00449999068581-1.43645713486E-60.533283961424-0.024503617067-0.02056903001780.458715297557-0.04502685786960.500471286763-65.9483358947-24.9118815434-7.81296357351
30.2350292415450.1101061362910.2013292671490.0499743505550.09807506961980.1437890831110.0009965908817671.17078915175-0.245069968307-0.4227510169220.347027745593-0.6099355611630.08948021550231.046504434170.00124652611470.5814371932370.04730715437620.02244569849770.858355588372-0.2126441450320.815193592014-32.6324050041-25.6859587531.17841169846
40.116502744710.0400141387047-0.02989890071550.0570585546305-0.06006757915290.199867326959-0.4382894362870.2452935614631.033869987440.04556439298240.3833736045070.416718700299-0.132887272745-0.739836392815-0.02207976491280.5317829907640.04107210852910.07123244996830.7378499317090.07388838293470.994018556162-0.0939493810999-40.1626863281-0.579651039829
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 405 through 1135 )AA405 - 11351 - 347
22chain 'A' and (resid 1136 through 1525 )AA1136 - 1525348 - 737
33chain 'C' and (resid 1 through 10 )CC1 - 10
44chain 'C' and (resid 11 through 20 )CC11 - 20

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