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- PDB-7zjr: X-ray structure of the periplasmic region of PilJ from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7zjr
TitleX-ray structure of the periplasmic region of PilJ from P. aeruginosa
ComponentsProtein PilJ
KeywordsSIGNALING PROTEIN / pilJ / Signal mechanotransduction / chemoreceptor-like / twitching motility protein / two-components system / methyl-accepting-chemotaxis-protein MCP homolog
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50312151016 Å
AuthorsPierrat, X. / Pojer, F. / Persat, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_189084 Switzerland
CitationJournal: To Be Published
Title: X-ray structure of the periplasmic region of PilJ from P. aeruginosa
Authors: Pierrat, X. / Pojer, F. / Persat, A.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Protein PilJ


Theoretical massNumber of molelcules
Total (without water)31,7591
Polymers31,7591
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: molecular dynamics with a model of full length pilJ, unpublished mutagenesis on the dimerization interface, unpublished
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.059, 80.059, 202.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Protein PilJ


Mass: 31759.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pilJ, PA0411 / Plasmid: pXP209 - 6xHis_Thrombin_PilJ_periplasmic / Details (production host): PilJ(36-309) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P42257
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% v/v Jeffamine M-600 pH 7.0, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→49.4400799314 Å / Num. obs: 54408 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 64.6291655926 Å2 / Rrim(I) all: 0.068 / Net I/σ(I): 21.36
Reflection shellResolution: 2.32→2.46 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 8751 / CC1/2: 0.45 / Rrim(I) all: 1.96

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yfa

2yfa


Resolution: 2.50312151016→49.4400799314 Å / SU ML: 0.364286546272 / Cross valid method: FREE R-VALUE / σ(F): 1.3400428594 / Phase error: 27.4485563934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245240172751 1157 4.90254237288 %
Rwork0.215074867602 22443 -
obs0.216598906847 23600 99.9280179532 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.1813474692 Å2
Refinement stepCycle: LAST / Resolution: 2.50312151016→49.4400799314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 0 14 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008560389988072076
X-RAY DIFFRACTIONf_angle_d0.9035408052132812
X-RAY DIFFRACTIONf_chiral_restr0.0531722816143323
X-RAY DIFFRACTIONf_plane_restr0.00498175339753380
X-RAY DIFFRACTIONf_dihedral_angle_d19.66919116531275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.50312151016-2.6170.3699773810531270.3128379395732727X-RAY DIFFRACTION99.6160558464
2.617-2.7550.3353522494231480.2996267384492764X-RAY DIFFRACTION99.9656711294
2.755-2.92760.3384053678821470.2725714950472711X-RAY DIFFRACTION100
2.9276-3.15360.3261901761691350.2847563288662795X-RAY DIFFRACTION99.9658819516
3.1536-3.47090.3130021459211340.2633693499142793X-RAY DIFFRACTION100
3.4709-3.97290.227468559061480.219766995422800X-RAY DIFFRACTION100
3.9729-5.00470.2386670450521430.1775338467952856X-RAY DIFFRACTION100
5.0047-49.440.1828672139851750.1767244253682997X-RAY DIFFRACTION99.8740554156

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