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- PDB-8phx: Receiver Domain of the Hybrid Histidine Kinase Sln1 of Candida al... -

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Basic information

Entry
Database: PDB / ID: 8phx
TitleReceiver Domain of the Hybrid Histidine Kinase Sln1 of Candida albicans
ComponentsHistidine protein kinase SLN1
KeywordsSIGNALING PROTEIN / hybrid histidine kinase / Fungal / phosphorelay / kinase
Function / homology
Function and homology information


cellular response to farnesol / positive regulation of filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to biotic stimulus / osmosensor activity / histidine phosphotransfer kinase activity / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay sensor kinase activity / histidine kinase / cell wall organization ...cellular response to farnesol / positive regulation of filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to biotic stimulus / osmosensor activity / histidine phosphotransfer kinase activity / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / phosphorelay sensor kinase activity / histidine kinase / cell wall organization / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Histidine kinase/HSP90-like ATPase / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain / 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. ...Histidine kinase/HSP90-like ATPase / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain / 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 protein kinase SLN1
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsParedes-Martinez, F. / Casino, P.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-110630GB-I00 Spain
CitationJournal: Commun Biol / Year: 2024
Title: Structural and functional insights underlying recognition of histidine phosphotransfer protein in fungal phosphorelay systems.
Authors: Paredes-Martinez, F. / Eixeres, L. / Zamora-Caballero, S. / Casino, P.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine protein kinase SLN1
B: Histidine protein kinase SLN1
C: Histidine protein kinase SLN1
D: Histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8058
Polymers58,7084
Non-polymers974
Water8,647480
1
A: Histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7012
Polymers14,6771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7012
Polymers14,6771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7012
Polymers14,6771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7012
Polymers14,6771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.163, 96.272, 97.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Histidine protein kinase SLN1


Mass: 14676.970 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: SLN1, CAALFM_CR01000CA, CaO19.10766, CaO19.3256 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5A872, histidine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % w/v PEG 4000 0.1 M Tris-HCl pH 8.5 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→97.28 Å / Num. obs: 98531 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Χ2: 1.01 / Net I/σ(I): 17.3 / Num. measured all: 723181
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.995 / Num. measured all: 35636 / Num. unique obs: 4803 / CC1/2: 0.749 / Rpim(I) all: 0.386 / Rrim(I) all: 1.069 / Χ2: 1 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→54.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21521 4801 4.9 %RANDOM
Rwork0.19328 ---
obs0.19435 93665 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2--0.3 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 4 482 4455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124053
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164064
X-RAY DIFFRACTIONr_angle_refined_deg1.361.6245475
X-RAY DIFFRACTIONr_angle_other_deg0.7551.5689384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.17511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83210794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024646
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02838
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_it1.4321.8412082
X-RAY DIFFRACTIONr_mcbond_other1.4161.8412082
X-RAY DIFFRACTIONr_mcangle_it2.153.3032601
X-RAY DIFFRACTIONr_mcangle_other2.153.3042602
X-RAY DIFFRACTIONr_scbond_it2.9412.241971
X-RAY DIFFRACTIONr_scbond_other2.942.2411972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5913.942864
X-RAY DIFFRACTIONr_long_range_B_refined6.13321.854635
X-RAY DIFFRACTIONr_long_range_B_other5.720.174531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 349 -
Rwork0.25 6826 -
obs--99.99 %

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