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- PDB-9of3: Structure of the Acinetobacter baumannii Response Regulator PmrA ... -

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Basic information

Entry
Database: PDB / ID: 9of3
TitleStructure of the Acinetobacter baumannii Response Regulator PmrA Receiver Domain D10N 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: 2.67 Å
AuthorsJaimes, F.E. / Milton, M.E. / Hondros, A.D. / Kinkead, J. / 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
E: PmrA
F: PmrA
G: PmrA
H: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43810
Polymers115,3908
Non-polymers492
Water25214
1
A: PmrA
E: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8723
Polymers28,8472
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PmrA
F: PmrA


Theoretical massNumber of molelcules
Total (without water)28,8472
Polymers28,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PmrA
G: PmrA


Theoretical massNumber of molelcules
Total (without water)28,8472
Polymers28,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PmrA
H: PmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8723
Polymers28,8472
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.742, 109.742, 214.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 14423.700 Da / Num. of mol.: 8 / Mutation: D10N
Source method: isolated from a genetically manipulated source
Details: pET28a fusion protein cleaved with thrombin protease
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: 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.: 14 / 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 Matthews: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M NH4PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 37963 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 32.31 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 2.67→2.72 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1787 / CC1/2: 0.964 / CC star: 0.991

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Processing

Software
NameVersionClassification
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→48.84 Å / SU ML: 0.3427 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 30.6685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 1952 5.29 %
Rwork0.2245 34954 -
obs0.2271 36906 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.96 Å2
Refinement stepCycle: LAST / Resolution: 2.67→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7586 0 2 14 7602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227688
X-RAY DIFFRACTIONf_angle_d0.465610373
X-RAY DIFFRACTIONf_chiral_restr0.041220
X-RAY DIFFRACTIONf_plane_restr0.01421323
X-RAY DIFFRACTIONf_dihedral_angle_d13.98092925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.740.37251310.3072328X-RAY DIFFRACTION92.83
2.74-2.810.33511320.29612425X-RAY DIFFRACTION95.95
2.81-2.890.36181380.29212429X-RAY DIFFRACTION96.61
2.89-2.990.321360.2762437X-RAY DIFFRACTION97.02
2.99-3.090.3291410.262477X-RAY DIFFRACTION98.02
3.09-3.220.30771390.25382494X-RAY DIFFRACTION98.21
3.22-3.360.34651390.24912504X-RAY DIFFRACTION98.4
3.36-3.540.2881400.24472526X-RAY DIFFRACTION98.63
3.54-3.760.25051380.22582472X-RAY DIFFRACTION97.13
3.76-4.050.27171390.21012536X-RAY DIFFRACTION98.93
4.05-4.460.25261430.17242562X-RAY DIFFRACTION99.3
4.46-5.110.18561450.15672591X-RAY DIFFRACTION99.45
5.11-6.430.2281470.20792601X-RAY DIFFRACTION98.71
6.43-48.840.24751440.20692572X-RAY DIFFRACTION92.04
Refinement TLS params.Method: refined / Origin x: 3.27563288203 Å / Origin y: 20.9594363299 Å / Origin z: 27.0601636059 Å
111213212223313233
T0.235462556632 Å20.00106558736572 Å20.00416310120229 Å2-0.226092546997 Å20.010592319247 Å2--0.139009190157 Å2
L0.422504049666 °2-0.0182706788926 °20.00403255963481 °2-0.144022983225 °20.00172252290643 °2--0.0517700657992 °2
S0.0281969990397 Å °-0.0248970311365 Å °-0.0435142585686 Å °0.00890606417991 Å °-0.0205973075926 Å °0.00206766525232 Å °-0.0328303373084 Å °-0.0211763450473 Å °-0.00818975306711 Å °
Refinement TLS groupSelection details: all

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