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- PDB-9of6: Structure of the Acinetobacter baumannii Response Regulator PmrA ... -

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Basic information

Entry
Database: PDB / ID: 9of6
TitleStructure of the Acinetobacter baumannii Response Regulator PmrA Receiver Domain I13M Mutation in Active Dimer State
ComponentsPmrA
KeywordsTRANSCRIPTION / Response regulator / two component system / Polymyxin resistance / Resistant mutant
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMilton, M.E. / Jaimes, F.E. / Cavanagh, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136904 United States
CitationJournal: Microorganisms / Year: 2025
Title: PmrA Mutations in Drug-Resistant Acinetobacter baumannii Affect Sensor Kinase-Response Regulator Interaction and Phosphotransfer
Authors: Jaimes, F.E. / Hondros, A.D. / Kinkead, J. / Milton, M.E. / Thompson, R.J. / Figg, A.M. / Melander, C. / Cavanagh, J.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PmrA
B: PmrA


Theoretical massNumber of molelcules
Total (without water)28,8852
Polymers28,8852
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Dimer interface established for receiver domains of other response regulator proteins.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.137, 35.517, 92.118
Angle α, β, γ (deg.)90.000, 92.876, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PmrA / Transcriptional regulator / Two-component system DNA-binding response regulator / Two-component ...Transcriptional regulator / Two-component system DNA-binding response regulator / Two-component system response regulator QseB


Mass: 14442.724 Da / Num. of mol.: 2 / Mutation: I13M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: 19606
Gene: pmrA, basR_1, basR_2, qseB, qseB_2, A7M90_18170, ABR2091_2956, ABUW_0828, AUO97_02740, B9W25_09955, B9X95_17090, CBE85_16420, DWA16_01580, EJ062_06180, F2P40_15420, F4T83_01935, FJU42_11495, ...Gene: pmrA, basR_1, basR_2, qseB, qseB_2, A7M90_18170, ABR2091_2956, ABUW_0828, AUO97_02740, B9W25_09955, B9X95_17090, CBE85_16420, DWA16_01580, EJ062_06180, F2P40_15420, F4T83_01935, FJU42_11495, FPK81_16510, FQZ18_03960, G3N53_18550, GNY86_16835, GSE42_16350, IAG11_11965, IHV20_16245, J6E47_03800, JHZ39_002196, LV35_02798, MKP18_003095, SAMEA104305318_02859, SAMEA4394745_03473
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2FGC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate pH 4.6, 30% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 18528 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 17.27 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.043 / Rrim(I) all: 0.106 / Rsym value: 0.096 / Net I/σ(I): 35.605
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 10.262 / Num. unique obs: 893 / CC1/2: 0.957 / CC star: 0.989 / Rpim(I) all: 0.133 / Rrim(I) all: 0.31 / Rsym value: 0.279 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
JBluIce-EPICSdata collection
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→46 Å / SU ML: 0.1914 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.3882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1842 9.95 %
Rwork0.1798 16662 -
obs0.1846 18504 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.91 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 122 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521992
X-RAY DIFFRACTIONf_angle_d0.75112687
X-RAY DIFFRACTIONf_chiral_restr0.0462314
X-RAY DIFFRACTIONf_plane_restr0.0056345
X-RAY DIFFRACTIONf_dihedral_angle_d13.359761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.26911080.19311044X-RAY DIFFRACTION81.24
1.91-1.970.22031580.19361311X-RAY DIFFRACTION99.86
1.97-2.030.25821340.19221262X-RAY DIFFRACTION99.64
2.03-2.10.29691370.18781295X-RAY DIFFRACTION99.65
2.1-2.190.2651430.18221275X-RAY DIFFRACTION99.58
2.19-2.290.26471460.18131286X-RAY DIFFRACTION99.72
2.29-2.410.22161360.16641308X-RAY DIFFRACTION99.86
2.41-2.560.22831420.17771299X-RAY DIFFRACTION99.79
2.56-2.760.24581450.18561295X-RAY DIFFRACTION99.93
2.76-3.040.20611540.18621290X-RAY DIFFRACTION99.86
3.04-3.470.25751460.17991304X-RAY DIFFRACTION99.79
3.47-4.380.18271490.16811325X-RAY DIFFRACTION99.86
4.38-460.21371440.17881368X-RAY DIFFRACTION99.47

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