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- PDB-8rqj: Histidine-containing phosphotransfer protein from Chaetomium term... -

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Basic information

Entry
Database: PDB / ID: 8rqj
TitleHistidine-containing phosphotransfer protein from Chaetomium termophilum mutant R158A
ComponentsHPt domain-containing protein
KeywordsTRANSFERASE / Histidine-containing transferase / fungal / Phosphorelay
Function / homology
Function and homology information


protein histidine kinase binding / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / nucleus / 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
Similarity search - Domain/homology
HPt domain-containing protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsParedes-Martinez, F. / Casino, P.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-141621NB-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
DepositionJan 18, 2024Deposition 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

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Assembly

Deposited unit
B: HPt domain-containing protein
A: HPt domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7693
Polymers37,6732
Non-polymers961
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-19 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.350, 123.156, 128.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein HPt domain-containing protein


Mass: 18836.629 Da / Num. of mol.: 2 / Mutation: R158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0013690 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle-T7 / References: UniProt: G0S1I2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Ammonium Sulfate 1.0 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→72 Å / Num. obs: 6876 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.076 / Rrim(I) all: 0.269 / Χ2: 0.97 / Net I/σ(I): 8.8
Reflection shellResolution: 3.4→3.67 Å / Rmerge(I) obs: 1.971 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1389 / CC1/2: 0.759 / Rpim(I) all: 0.559 / Rrim(I) all: 2.049 / Χ2: 0.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 42.033 / SU ML: 0.593 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30189 333 4.8 %RANDOM
Rwork0.24384 ---
obs0.24669 6543 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.945 Å2
Baniso -1Baniso -2Baniso -3
1-7.64 Å2-0 Å2-0 Å2
2--4.44 Å20 Å2
3----12.07 Å2
Refinement stepCycle: 1 / Resolution: 3.4→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 5 8 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161712
X-RAY DIFFRACTIONr_angle_refined_deg0.8071.6122537
X-RAY DIFFRACTIONr_angle_other_deg0.2841.5613920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.94152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07110242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0350.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
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_it5.88111.8471038
X-RAY DIFFRACTIONr_mcbond_other5.88111.8481038
X-RAY DIFFRACTIONr_mcangle_it9.87621.2951294
X-RAY DIFFRACTIONr_mcangle_other9.87521.2921295
X-RAY DIFFRACTIONr_scbond_it6.31812.493825
X-RAY DIFFRACTIONr_scbond_other6.32912.489822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.88422.7751238
X-RAY DIFFRACTIONr_long_range_B_refined19.563141.458149
X-RAY DIFFRACTIONr_long_range_B_other19.564141.458147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 10 -
Rwork0.409 495 -
obs--99.8 %

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