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- PDB-7m0s: N-terminal domain of PmrA from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 7m0s
TitleN-terminal domain of PmrA from Acinetobacter baumannii
ComponentsTwo-component system response regulator PmrATwo-component regulatory system
KeywordsTRANSCRIPTION / colistin resistance
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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
Two-component system response regulator
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPalethorpe, S. / Milton, M.E. / Cavanagh, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136904-01A1 United States
CitationJournal: J.Biochem. / Year: 2022
Title: Structure of the Acinetobacter baumannii PmrA receiver domain and insights into clinical mutants affecting DNA binding and promoting colistin resistance.
Authors: Palethorpe, S. / Milton, M.E. / Pesci, E.C. / Cavanagh, J.
History
DepositionMar 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component system response regulator PmrA
B: Two-component system response regulator PmrA


Theoretical massNumber of molelcules
Total (without water)28,8492
Polymers28,8492
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: OmpR/PhoP family response regulators, of which PmrA is a member, are known to form homodimers in solution and within a cyrstal lattice.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.398, 39.232, 91.266
Angle α, β, γ (deg.)90.000, 95.660, 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 Two-component system response regulator PmrA / Two-component regulatory system


Mass: 14424.685 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: pmrA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DEH3) / References: UniProt: A0A517D2C4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 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: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 27942 / % possible obs: 98.3 % / Redundancy: 6.1 % / CC1/2: 0.939 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.828
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 10.75 / Num. unique obs: 1293 / CC1/2: 0.939 / Rsym value: 0.162 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.18rc6-3830refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18rc6-3830phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ONT

6ont


Resolution: 1.64→45.41 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 2005 7.19 %
Rwork0.1741 --
obs0.1769 27883 97.96 %
Displacement parametersBiso mean: 18.68 Å2
Refinement stepCycle: LAST / Resolution: 1.64→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 0 227 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012046
X-RAY DIFFRACTIONf_angle_d1.0772767
X-RAY DIFFRACTIONf_chiral_restr0.0596324
X-RAY DIFFRACTIONf_plane_restr0.0068356
X-RAY DIFFRACTIONf_dihedral_angle_d19.9032787
LS refinement shellResolution: 1.64→1.68 Å / Rfactor Rfree: 0.2646 / Rfactor Rwork: 0.2023

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