+Open data
-Basic information
Entry | Database: PDB / ID: 8i25 | ||||||
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Title | NMR structure of Toxoplasma gondii PDCD5 (trans form) | ||||||
Components | Programmed cell death 5 protein | ||||||
Keywords | ENDOCYTOSIS / Molten globule / Heparan sulfate/Heparin binding protein / Proline trans form | ||||||
Function / homology | PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / nucleus / cytosol / Programmed cell death 5 protein Function and homology information | ||||||
Biological species | Toxoplasma gondii GT1 (eukaryote) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Lin, M.H. / Hsu, C.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i25.cif.gz | 858.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i25.ent.gz | 730.3 KB | Display | PDB format |
PDBx/mmJSON format | 8i25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i25_validation.pdf.gz | 409.9 KB | Display | wwPDB validaton report |
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Full document | 8i25_full_validation.pdf.gz | 566.5 KB | Display | |
Data in XML | 8i25_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 8i25_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i25 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i25 | HTTPS FTP |
-Related structure data
Related structure data | 8i26C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13716.472 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Authors only can superimpose a part of the structure with good rmsd. 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | 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. Ionic strength: 125 mM / Label: 1 / pH: 4.5 / Pressure: 1 atm / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100000 / Conformers submitted total number: 20 |