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- PDB-7z8n: GacS histidine kinase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7z8n
TitleGacS histidine kinase from Pseudomonas aeruginosa
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / Histidine Kinase HAMP domain Coiled-coil GacS Pseudomonas aeruginosa
Function / homology
Function and homology information


positive regulation of secondary metabolite biosynthetic process / positive regulation of cell motility / histidine kinase / phosphorelay sensor kinase activity / plasma membrane
Similarity search - Function
Histidine kinase BarA, N-terminal / Single cache domain 4 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Histidine kinase BarA, N-terminal / Single cache domain 4 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
R-1,2-PROPANEDIOL / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsFadel, F. / Bassim, V. / Francis, V.I. / Porter, S.L. / Botzanowski, T. / Legrand, P. / Bourne, Y. / Cianferani, S. / Vincent, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Structure / Year: 2022
Title: Insights into the atypical autokinase activity of the Pseudomonas aeruginosa GacS histidine kinase and its interaction with RetS.
Authors: Fadel, F. / Bassim, V. / Francis, V.I. / Porter, S.L. / Botzanowski, T. / Legrand, P. / Perez, M.M. / Bourne, Y. / Cianferani, S. / Vincent, F.
History
DepositionMar 17, 2022Deposition site: PDBE / Processing site: PDBE
SupersessionJul 13, 2022ID: 6ZLS
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase
B: Histidine kinase
C: Histidine kinase
D: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,90610
Polymers141,5584
Non-polymers3496
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.710, 76.850, 178.650
Angle α, β, γ (deg.)90.000, 97.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Histidine kinase


Mass: 35389.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The protein sequence has been produced with a histidine tag followed by a TEV protease cleavage site. This part of the protein is not modelled and does not appear in the PDB sequence.
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gacS, PA0928 / Plasmid: pLIC03 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD98, histidine kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium chloride 24% PEG 3350 0.1M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.64→48.81 Å / Num. obs: 45042 / % possible obs: 89 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 16
Reflection shellResolution: 2.64→2.71 Å / Num. unique obs: 2252 / CC1/2: 0.429

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.64→48.81 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.773 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.705 / SU Rfree Blow DPI: 0.318 / SU Rfree Cruickshank DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 2266 5.03 %RANDOM
Rwork0.2592 ---
obs0.2594 45042 89 %-
Displacement parametersBiso max: 257.25 Å2 / Biso mean: 95.9 Å2 / Biso min: 35.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.1734 Å20 Å21.0352 Å2
2---5.7291 Å20 Å2
3---2.5557 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.64→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9032 0 18 178 9228
Biso mean--91.47 67.18 -
Num. residues----1168
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3447SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1639HARMONIC5
X-RAY DIFFRACTIONt_it9213HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1254SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6912SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9213HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg12447HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion19.15
LS refinement shellResolution: 2.64→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4221 45 4.99 %
Rwork0.3253 856 -
all0.33 901 -
obs--46.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4098-0.36840.29790.91340.6310.9205-0.00850.31120.0564-0.1124-0.0879-0.0118-0.11750.21530.09640.0030.10340.05030.03130.1197-0.0778-110.835335.0503144.1506
21.12230.11980.01310.2714-0.08270.09230.0826-0.4015-0.0748-0.0501-0.03230.0333-0.00770.0681-0.0502-0.013-0.03920.05680.01420.0055-0.0179-7.953836.057327.2031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|256 - A|512 D|256 - D|512 }A256 - 512
2X-RAY DIFFRACTION1{ A|256 - A|512 D|256 - D|512 }D256 - 512
3X-RAY DIFFRACTION2{ B|256 - B|512 C|256 - C|512 }B256 - 512
4X-RAY DIFFRACTION2{ B|256 - B|512 C|256 - C|512 }C256 - 512

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