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- PDB-1yyb: Solution structure of 1-26 fragment of human programmed cell deat... -

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Basic information

Entry
Database: PDB / ID: 1yyb
TitleSolution structure of 1-26 fragment of human programmed cell death 5 protein
ComponentsProgrammed cell death protein 5
KeywordsAPOPTOSIS / PDCD5(1-26) / solution structure
Function / homology
Function and homology information


positive regulation of protein insertion into mitochondrial outer membrane / negative regulation of chaperone-mediated protein folding / acetyltransferase activator activity / beta-tubulin binding / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to transforming growth factor beta stimulus / heparin binding / positive regulation of apoptotic process / negative regulation of cell population proliferation ...positive regulation of protein insertion into mitochondrial outer membrane / negative regulation of chaperone-mediated protein folding / acetyltransferase activator activity / beta-tubulin binding / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to transforming growth factor beta stimulus / heparin binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / apoptotic process / positive regulation of gene expression / DNA binding / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain
Similarity search - Domain/homology
Programmed cell death protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiu, D.S. / Feng, Y.G. / Yao, H.W. / Wang, J.F.
CitationJournal: Biochem.J. / Year: 2005
Title: The N-terminal 26-residue fragment of human programmed cell death 5 protein can form a stable alpha-helix having unique electrostatic potential character.
Authors: Liu, D. / Yao, H. / Chen, Y. / Feng, Y. / Chen, Y. / Wang, J.
History
DepositionFeb 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 5


Theoretical massNumber of molelcules
Total (without water)2,9671
Polymers2,9671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #4lowest energy

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Components

#1: Protein/peptide Programmed cell death protein 5 / PDCD5 / TFAR19 protein / TF-1 cell apoptosis related gene-19 protein


Mass: 2967.190 Da / Num. of mol.: 1 / Fragment: residues 2-26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14737

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N NOESY-HSQC; 3D 15N TOCSY-HSQC; 2D 15N HSQC
1222D 13C HMQC; HMQC-NOESY; HMQC-TOCSY
1332D TOCSY; 2D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12-4mM PDCD5(1-26)-15N labeled; 50mM Phosphate buffer, 200mM NaCl, DSS, NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
22mM PDCD5(1-26)-13C labeled; 50mM Phosphate buffer, 200mM NaCl, DSS, NaN3; 100% D2O100% D2O
32-4mM unlabeled PDCD5(1-26); 50mM Phosphate buffer, 200mM NaCl, DSS, NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.25 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Felix98MSIdata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 223 intraredidual,sequential and medium range NOE restraints, and 19 phi and 19 psi dihedral angle restraints driving from programe TALOS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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