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- PDB-6f8e: PH domain from TgAPH -

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Basic information

Entry
Database: PDB / ID: 6f8e
TitlePH domain from TgAPH
ComponentsPleckstrin homology domain
KeywordsLIPID BINDING PROTEIN / PH domain / phosphatidic acid binding / membrane association
Function / homologyPH-like domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsDarvill, N. / Liu, B. / Matthews, S. / Soldati-Favre, D. / Rouse, S. / Benjamin, S. / Blake, T. / Dubois, D.J. / Hammoudi, P.M. / Pino, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust105394/Z/14/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites.
Authors: Darvill, N. / Dubois, D.J. / Rouse, S.L. / Hammoudi, P.M. / Blake, T. / Benjamin, S. / Liu, B. / Soldati-Favre, D. / Matthews, S.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleckstrin homology domain


Theoretical massNumber of molelcules
Total (without water)13,7601
Polymers13,7601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Purifies as a single monomer under reducing conditions
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Pleckstrin homology domain


Mass: 13759.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: TGME49_249970 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125YY72

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D HBHA(CO)NH
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 730 uM [U-100% 15N]; [U-100% 13C] C-terminal PH domain from TgAPH, 90% H2O/10% D2O
Label: 15N_13C_TgAPH / Solvent system: 90% H2O/10% D2O
SampleConc.: 730 uM / Component: C-terminal PH domain from TgAPH / Isotopic labeling: [U-100% 15N]; [U-100% 13C]
Sample conditionsIonic strength: 150 NaCl mM / Label: 3D_NMR_conditions / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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