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- PDB-8pdc: Complex of Histidine-containing phosphotransfer protein and recei... -

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Basic information

Entry
Database: PDB / ID: 8pdc
TitleComplex of Histidine-containing phosphotransfer protein and receiver domain of hybrid Histidine Kinase 6 from Chaetomium thermophilum
Components
  • HPt domain-containing protein
  • histidine kinase
KeywordsSIGNALING PROTEIN / Histidine-containing phosphotransferase / hybrid Histidine Kinase / Fungal / Phosphorelay / TRANSFERASE / kinase
Function / homology
Function and homology information


protein histidine kinase binding / histidine phosphotransfer kinase activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / nucleus / membrane / cytoplasm
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Histidine kinase/HSP90-like ATPase / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain ...Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Histidine kinase/HSP90-like ATPase / 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
BERYLLIUM TRIFLUORIDE ION / HPt domain-containing protein / histidine kinase
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 12, 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
B: HPt domain-containing protein
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8624
Polymers34,7722
Non-polymers902
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-12 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.251, 57.469, 68.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HPt domain-containing protein


Mass: 18922.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0013690 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: G0S1I2
#2: Protein histidine kinase


Mass: 15849.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0050920 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: G0SD89
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.65 Å3/Da / Density meas: 25.66 Mg/m3
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulphate 1 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→68.97 Å / Num. obs: 9386 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Χ2: 0.99 / Net I/σ(I): 9.2 / Num. measured all: 66052
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.971 / Num. measured all: 7181 / Num. unique obs: 975 / CC1/2: 0.792 / Rpim(I) all: 0.388 / Rrim(I) all: 1.047 / Χ2: 0.97 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R25

2r25


Resolution: 2.4→44.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.042 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.65 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26794 471 5 %RANDOM
Rwork0.22031 ---
obs0.22257 8874 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.106 Å2
Baniso -1Baniso -2Baniso -3
1-6.16 Å20 Å20 Å2
2---2.69 Å20 Å2
3----3.47 Å2
Refinement stepCycle: 1 / Resolution: 2.4→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 5 19 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161848
X-RAY DIFFRACTIONr_angle_refined_deg0.7421.6252571
X-RAY DIFFRACTIONr_angle_other_deg0.2631.5664242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.90657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25110316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0340.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
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_it1.5854.5351006
X-RAY DIFFRACTIONr_mcbond_other1.5854.5351006
X-RAY DIFFRACTIONr_mcangle_it2.7188.1461254
X-RAY DIFFRACTIONr_mcangle_other2.7178.1481255
X-RAY DIFFRACTIONr_scbond_it1.7714.652894
X-RAY DIFFRACTIONr_scbond_other1.7724.66892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0838.5321315
X-RAY DIFFRACTIONr_long_range_B_refined4.81543.72088
X-RAY DIFFRACTIONr_long_range_B_other4.81343.722086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 31 -
Rwork0.28 652 -
obs--100 %

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