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- PDB-9of4: Structure of the Acinetobacter baumannii Response Regulator PmrA ... -

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Basic information

Entry
Database: PDB / ID: 9of4
TitleStructure of the Acinetobacter baumannii Response Regulator PmrA Receiver Domain M12I Mutation
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: 2.08 Å
AuthorsJaimes, F.E. / Milton, M.E. / Hondros, A.D. / 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
C: PmrA
D: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6756
Polymers57,6274
Non-polymers492
Water1,58588
1
A: PmrA
B: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8383
Polymers28,8132
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PmrA
D: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8383
Polymers28,8132
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.575, 59.450, 93.930
Angle α, β, γ (deg.)90.000, 90.068, 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: 14406.647 Da / Num. of mol.: 4 / Mutation: M12I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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 % sol: 34.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 0.2 M MgCl2, 25% PEG 3350

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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: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 107064 / % possible obs: 96.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.069 / Rrim(I) all: 0.149 / Rsym value: 0.131 / Net I/σ(I): 25.693
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.723 / Num. unique obs: 1205 / CC1/2: 0.817 / CC star: 0.948 / Rpim(I) all: 0.26 / Rrim(I) all: 0.518 / Rsym value: 0.444 / % possible all: 93.3

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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: 2.08→38.57 Å / SU ML: 0.2396 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.5967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2786 1990 8.04 %
Rwork0.2223 22757 -
obs0.2266 24747 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.52 Å2
Refinement stepCycle: LAST / Resolution: 2.08→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 2 88 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263994
X-RAY DIFFRACTIONf_angle_d0.5435396
X-RAY DIFFRACTIONf_chiral_restr0.0411638
X-RAY DIFFRACTIONf_plane_restr0.0168692
X-RAY DIFFRACTIONf_dihedral_angle_d4.9426530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.35581320.27031434X-RAY DIFFRACTION85.02
2.13-2.190.30121400.26471617X-RAY DIFFRACTION96.01
2.19-2.250.29151390.25641615X-RAY DIFFRACTION95.85
2.25-2.320.28711460.25391634X-RAY DIFFRACTION96.63
2.32-2.40.34781440.24631663X-RAY DIFFRACTION96.58
2.41-2.50.26841470.25041605X-RAY DIFFRACTION96.9
2.5-2.620.30081450.25921651X-RAY DIFFRACTION97.13
2.62-2.750.29281480.24671661X-RAY DIFFRACTION97.57
2.75-2.930.32091430.24881628X-RAY DIFFRACTION97.31
2.93-3.150.25981390.23121641X-RAY DIFFRACTION96.53
3.15-3.470.2461470.22091687X-RAY DIFFRACTION97.29
3.47-3.970.25371350.20191598X-RAY DIFFRACTION94.85
3.97-50.25381380.17111638X-RAY DIFFRACTION94.67
5-38.570.2741470.20721685X-RAY DIFFRACTION95.77

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