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- PDB-8i26: NMR structure of Toxoplasma gondii PDCD5 (cis form) -

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Basic information

Entry
Database: PDB / ID: 8i26
TitleNMR structure of Toxoplasma gondii PDCD5 (cis form)
ComponentsProgrammed cell death 5 protein
KeywordsENDOCYTOSIS / Molten globule / Heparan sulfate/Heparin binding protein / Proline cis form
Function / homologyPDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / nucleus / cytosol / Programmed cell death 5 protein
Function and homology information
Biological speciesToxoplasma gondii GT1 (eukaryote)
MethodSOLUTION NMR / distance geometry
AuthorsLin, M.H. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)110-2113-M-002-023 Taiwan
CitationJournal: Jacs Au / Year: 2024
Title: Proline Isomerization and Molten Globular Property of TgPDCD5 Secreted from Toxoplasma gondii Confers Its Regulation of Heparin Sulfate Binding.
Authors: Lin, G.M. / Yu, T.A. / Chang, C.F. / Hsu, C.H.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 5 protein


Theoretical massNumber of molelcules
Total (without water)13,7161
Polymers13,7161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Programmed cell death 5 protein


Mass: 13716.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii GT1 (eukaryote) / Gene: TGGT1_207690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125YJ71

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic33D HN(CA)CB
121anisotropic33D CBCA(CO)NH
131anisotropic33D HNCA
141anisotropic33D HNCO
151anisotropic32D 1H-15N HSQC
161anisotropic33D 1H-13C NOESY
171anisotropic33D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] Protein, 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM sodium azide, 1 mM PMSF, 90% H2O/10% D2O
Details: The purified protein was concentrated to 0.1-0.5 mM in buffer 25 mM sodium phosphate, 100 mM NaCl, 10 mM sodium azide and 1mM PMSF with pH 4.5 for NMR.
Label: 15N_sample, 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMProtein[U-100% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
10 mMsodium azidenatural abundance1
1 mMPMSFnatural abundance1
Sample conditionsDetails: The purified protein was concentrated to 0.1-0.5 mM in buffer 25 mM sodium phosphate, 100 mM NaCl, 10 mM sodium azide and 1mM PMSF with pH 4.5 for NMR.
Ionic strength: 125 mM / Label: cis form / pH: 4.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100000 / Conformers submitted total number: 20

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