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- PDB-8phn: Receiver domain from hybrid Histidine Kinase 3 from Chaetomium th... -

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Basic information

Entry
Database: PDB / ID: 8phn
TitleReceiver domain from hybrid Histidine Kinase 3 from Chaetomium thermophilum
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / hybrid Histidine Kinase / Fungal / Phosphorelay / Kinase
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / membrane
Similarity search - Function
HAMP domain / HAMP domain / Histidine kinase/HSP90-like ATPase / 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-related protein, C-terminal ...HAMP domain / HAMP domain / Histidine kinase/HSP90-like ATPase / 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-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
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5313
Polymers15,4111
Non-polymers1202
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.268, 154.268, 154.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-1302-

SO4

21A-1302-

SO4

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Components

#1: Protein histidine kinase


Mass: 15410.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0053860 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: G0SBK1, histidine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2M ammonium sulphate 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: ALBA / Beamline: XALOC / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.9→89.07 Å / Num. obs: 12954 / % possible obs: 100 % / Redundancy: 21.3 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.02 / Rrim(I) all: 0.09 / Χ2: 0.98 / Net I/σ(I): 22.3 / Num. measured all: 275556
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 21.7 % / Rmerge(I) obs: 1.245 / Num. measured all: 17418 / Num. unique obs: 803 / CC1/2: 0.836 / Rpim(I) all: 0.272 / Rrim(I) all: 1.275 / Χ2: 0.95 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→89.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.979 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 683 5.3 %RANDOM
Rwork0.2111 ---
obs0.21169 12254 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: 35.699 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→89.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 6 45 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.012949
X-RAY DIFFRACTIONr_bond_other_d0.0010.016951
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.6331286
X-RAY DIFFRACTIONr_angle_other_deg0.3971.5632186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.25654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89410167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
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_it3.0153.565495
X-RAY DIFFRACTIONr_mcbond_other2.9723.563495
X-RAY DIFFRACTIONr_mcangle_it4.7596.39617
X-RAY DIFFRACTIONr_mcangle_other4.7656.395618
X-RAY DIFFRACTIONr_scbond_it3.8173.884454
X-RAY DIFFRACTIONr_scbond_other3.823.884451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2646.948664
X-RAY DIFFRACTIONr_long_range_B_refined8.2134.361016
X-RAY DIFFRACTIONr_long_range_B_other8.20334.371007
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 55 -
Rwork0.261 884 -
obs--100 %

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