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- PDB-7qz2: Crystal structure of GacS D1 domain in complex with BeF3- -

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Basic information

Entry
Database: PDB / ID: 7qz2
TitleCrystal structure of GacS D1 domain in complex with BeF3-
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / transmitter domain histidine kinase Pseudomonas aeruginosa
Function / homology
Function and homology information


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
BERYLLIUM TRIFLUORIDE ION / : / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 30, 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 1.2Feb 7, 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: Histidine kinase
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0899
Polymers34,5712
Non-polymers5187
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-27 kcal/mol
Surface area12880 Å2
Unit cell
Length a, b, c (Å)69.695, 74.016, 93.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-986-

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: The protein sequence is preceded by a histidine TAG followed by residues from the template plasmid and a TEV protease clivage site ENLYFQS. We don't see those residues 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.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 293 K / Method: evaporation
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 Then soaking those crystals into in 5 mM BeSO4, 30 mM NaF, 7 mM MgCl2 and 10 mM Tris-HCl pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9799 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: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.87→46.67 Å / Num. obs: 20248 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Net I/σ(I): 15.6
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.698 / Num. unique obs: 1224 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMN

3mmn


Resolution: 1.87→44.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.998 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21264 983 4.9 %RANDOM
Rwork0.16843 ---
obs0.17058 19241 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.278 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.87→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 13 201 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0142094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171925
X-RAY DIFFRACTIONr_angle_refined_deg1.331.6532854
X-RAY DIFFRACTIONr_angle_other_deg0.9081.6284519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88722.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1461519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0672.1531060
X-RAY DIFFRACTIONr_mcbond_other2.0642.151059
X-RAY DIFFRACTIONr_mcangle_it3.0023.2091327
X-RAY DIFFRACTIONr_mcangle_other3.0013.2121328
X-RAY DIFFRACTIONr_scbond_it2.9582.5471034
X-RAY DIFFRACTIONr_scbond_other2.9612.5521029
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5943.6831518
X-RAY DIFFRACTIONr_long_range_B_refined6.36326.5362316
X-RAY DIFFRACTIONr_long_range_B_other6.28226.0922261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.871→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 72 -
Rwork0.249 1325 -
obs--95.55 %

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