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- PDB-7qzo: Crystal structure of GacS D1 domain -

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Basic information

Entry
Database: PDB / ID: 7qzo
TitleCrystal structure of GacS D1 domain
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / receiver domain histidine kinase Pseudomonas aeruginosa
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / 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 / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 superfamily
Similarity search - Domain/homology
: / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFadel, F. / Bassim, V. / Botzanowski, T. / Francis, V.I. / Legrand, P. / Porter, S.L. / Bourne, Y. / Cianferani, S. / Vincent, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0005-01 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
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 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
Revision 1.2Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,2258
Polymers34,5712
Non-polymers6546
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-30 kcal/mol
Surface area13320 Å2
Unit cell
Length a, b, c (Å)69.152, 73.532, 104.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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Components

#1: Protein Histidine kinase


Mass: 17285.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 0 to 24 comprise a histidine TAG and a TEV protease clivage site that are not seen in the structure. residues in C-terminal QSL are also not present in the structure.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: gacS, PAMH19_4268 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A8RMX6, histidine kinase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M to 1.2 M Na acetate and 0.1 M HEPES from pH 7 to pH 8 in presence of 50 mM cadmium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.45→36.79 Å / Num. obs: 47424 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.99 / Net I/σ(I): 11
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 2300 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMN

3mmn


Resolution: 1.45→36.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.64 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1535 2306 4.9 %RANDOM
Rwork0.131 ---
obs0.1321 45083 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.15 Å2 / Biso mean: 19.983 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2--0.6 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.45→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 11 221 2241
Biso mean--39.73 31.79 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132044
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171964
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6372779
X-RAY DIFFRACTIONr_angle_other_deg1.511.5744541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97122.252111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9941518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022284
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02398
X-RAY DIFFRACTIONr_rigid_bond_restr2.74632044
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 189 -
Rwork0.241 3256 -
all-3445 -
obs--99.22 %

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