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- PDB-2k6b: Solution structure of 1-112 fragment of human programmed cell dea... -

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Basic information

Entry
Database: PDB / ID: 2k6b
TitleSolution structure of 1-112 fragment of human programmed cell death 5 protein
ComponentsProgrammed cell death protein 5
KeywordsAPOPTOSIS / PDCD5 / Phosphoprotein
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, DNA-binding domain / PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsFeng, Y. / Yao, H. / Liu, D. / Wang, J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2009
Title: Structure-function correlation of human programmed cell death 5 protein.
Authors: Yao, H. / Xu, L. / Feng, Y. / Liu, D. / Chen, Y. / Wang, J.
History
DepositionJul 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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)12,6921
Polymers12,6921
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 12692.337 Da / Num. of mol.: 1 / Fragment: UNP residues 2-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD5, TFAR19 / Production host: Escherichia coli (E. coli) / References: UniProt: O14737

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HNCO
1713D H(CCO)NH
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11023D (H)CCH-TOCSY
11113D HN(CA)CO
11223D (H)CCH-COSY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-2.0 mM [U-13C; U-15N] pdcd5, 100 mM [U-2H] acetic acid, 100 mM sodium chloride, 0.01 % DSS, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.0-2.0 mM [U-13C] pdcd5, 100 mM [U-2H] acetic acid, 100 mM sodium chloride, 0.01 % DSS, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMpdcd5[U-13C; U-15N]1
100 mMacetic acid[U-2H]1
100 mMsodium chloride1
0.01 %DSS1
0.01 %sodium azide1
1.0 mMpdcd5[U-13C]2
100 mMacetic acid[U-2H]2
100 mMsodium chloride2
0.01 %DSS2
0.01 %sodium azide2
Sample conditionsIonic strength: 0.1 / pH: 4.7 / Pressure: ambient / Temperature: 308 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
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.data analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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