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- PDB-9nx5: Crystal Structure of a P. Aeruginosa Gyrase -

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Basic information

Entry
Database: PDB / ID: 9nx5
TitleCrystal Structure of a P. Aeruginosa Gyrase
ComponentsDNA gyrase subunit B,DNA gyrase subunit A
KeywordsDNA BINDING PROTEIN / Gyrase / Pseudomonas aeruginosa
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
DNA gyrase subunit A / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Biorxiv / Year: 2025
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8487
Polymers105,3991
Non-polymers4486
Water2,540141
1
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)211,69514
Polymers210,7992
Non-polymers89712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area9550 Å2
ΔGint-102 kcal/mol
Surface area77310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.159, 218.159, 108.803
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

#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: This is a GyrB-GyrA fusion protein as follows GSAAA(tag)-GyraB(397-806)-GGS(linker)-GyrA(2-525),This is a GyrB-GyrA fusion protein as follows GSAAA(tag)-GyraB(397-806)-GSS(linker)-GyrA(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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: .1M HEPES pH 7.5 26% MBP 5% PEG8K / Temp details: coldroom

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 59670 / % possible obs: 100 % / Redundancy: 15.7 % / Biso Wilson estimate: 50.06 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.026 / Rrim(I) all: 0.102 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 1.259 / Num. unique obs: 2934 / CC1/2: 0.785 / Rpim(I) all: 0.345 / Rrim(I) all: 1.307

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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: 2.4→48.76 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: There appears to be a great deal of motion between residues A1383 and A1476. These residues are crudely modeled.
RfactorNum. reflection% reflection
Rfree0.2567 2970 5 %
Rwork0.2418 56421 -
obs0.2426 59391 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.99 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 27 141 6711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326701
X-RAY DIFFRACTIONf_angle_d0.56299081
X-RAY DIFFRACTIONf_chiral_restr0.0421038
X-RAY DIFFRACTIONf_plane_restr0.00451190
X-RAY DIFFRACTIONf_dihedral_angle_d13.40452463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.2721320.29342544X-RAY DIFFRACTION96.09
2.44-2.480.30331400.28052637X-RAY DIFFRACTION98.86
2.48-2.530.31691400.2832630X-RAY DIFFRACTION99.21
2.53-2.580.28751360.27422627X-RAY DIFFRACTION99.25
2.58-2.630.26811420.2762665X-RAY DIFFRACTION99.4
2.63-2.690.30141370.28222635X-RAY DIFFRACTION99.25
2.69-2.750.31671400.30642654X-RAY DIFFRACTION99.29
2.75-2.820.30511400.30212643X-RAY DIFFRACTION99.39
2.82-2.890.29641390.29022655X-RAY DIFFRACTION99.32
2.89-2.980.2941410.27712679X-RAY DIFFRACTION99.72
2.98-3.070.30661400.25982673X-RAY DIFFRACTION99.79
3.07-3.180.24341400.26342669X-RAY DIFFRACTION99.68
3.18-3.310.29531420.25642699X-RAY DIFFRACTION99.86
3.31-3.460.25781410.26592684X-RAY DIFFRACTION99.86
3.46-3.640.2591420.23342700X-RAY DIFFRACTION99.79
3.64-3.870.24021420.21932705X-RAY DIFFRACTION99.89
3.87-4.170.21231430.20522708X-RAY DIFFRACTION99.76
4.17-4.590.19361450.1882731X-RAY DIFFRACTION99.93
4.59-5.250.24221440.20572752X-RAY DIFFRACTION100
5.26-6.620.23861480.26872792X-RAY DIFFRACTION99.9
6.62-48.760.2781560.23922939X-RAY DIFFRACTION99.55
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)
11.28194041884-0.8353606403460.6650257794453.88498188142-1.063459910231.707155753470.00216136099503-0.0780379067768-0.1087477430370.0953547581076-0.08651371263050.160625065409-0.00682406885817-0.278887079350.05815114458150.400972964502-0.0945914912890.02414104621610.543824955709-0.05477537298560.436511399727-21.3996354155-96.382579378148.1265791393
21.49128542598-0.6308811592630.2584645906071.49020843773-0.1282727711922.53771141828-0.147989524659-0.408216526069-0.2627415948020.1244101722270.224284904779-0.0160719784780.133690413186-0.312397448759-0.1924219904980.4313433653440.0141857792172-0.05719771036350.5957165540790.1539656386710.552084203037-49.0439935256-81.108915593718.9850133529
31.4535703407-0.2841161547290.5378772240610.292864984611-0.4324201909221.293711508010.01682867903620.0372506445090.1585490562520.0458773986596-0.08433116389690.158299185084-0.165792960531-0.189868875909-0.02950272193220.5103483097380.0131211105584-0.0668941652350.488711258282-0.06559695935740.479834743617-29.6959327922-82.890925819238.2887489249
41.59526298768-0.4063792899510.2046578857590.3721656003620.1074080769581.08249638023-0.0744315336011-0.137488007330.0526867165259-0.006684202304360.03308008793990.04467083877690.0594971816409-0.06629243298790.08450931949930.4278407816510.0130597521674-0.06066243470320.4185577192120.02519128249250.356315189958-9.54979740854-81.809255920217.3892983195
51.60783822423-0.3389895598430.2274558926251.695791322140.2129094662040.651715526907-0.04107660990350.231980738455-0.119088345006-0.155959011363-0.03887672548170.1259292659760.0233811395174-0.005036920027230.05473873183790.388435356090.0172712578651-0.0717689054930.3695757556960.05518587717920.292558592704-13.6059087612-87.3158955541-2.14672444861
61.835172046391.062635863191.187281925610.6915244195280.8826836217551.12780819114-0.948367991829-0.7487972291732.59959164770.21354216074-0.164682922245-0.0876091568596-1.17921715148-0.7249876617940.6540721032551.307648348060.341485276149-0.8230822073990.827574786931-0.3650223721042.02666590767-14.9082919515-36.228932057224.8793095807
70.59091825949-0.229620383256-0.03955631687660.2869705850650.640059144211.82176089352-0.006971582825460.2211433554590.374569597377-0.42581566075-0.1165390667840.0660540413052-0.4644631969250.1028885553790.2338919422690.423689937268-0.0579041675161-0.090027105490.3887027697220.1072453153840.510914017301-16.2139000172-60.32471572890.676881960794
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 404 through 579 )404 - 5791 - 160
22chain 'A' and (resid 580 through 686 )580 - 686161 - 267
33chain 'A' and (resid 687 through 787 )687 - 787268 - 359
44chain 'A' and (resid 788 through 1153 )788 - 1153360 - 511
55chain 'A' and (resid 1154 through 1389 )1154 - 1389512 - 745
66chain 'A' and (resid 1390 through 1468 )1390 - 1468746 - 809
77chain 'A' and (resid 1469 through 1525 )1469 - 1525810 - 866

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