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- PDB-2o71: Crystal structure of RAIDD DD -

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Basic information

Entry
Database: PDB / ID: 2o71
TitleCrystal structure of RAIDD DD
ComponentsDeath domain-containing protein CRADD
KeywordsAPOPTOSIS / RAIDD / Death Domain
Function / homology
Function and homology information


death domain binding / endopeptidase complex / TP53 Regulates Transcription of Caspase Activators and Caspases / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of apoptotic signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / apoptotic signaling pathway / cellular response to mechanical stimulus / protein-macromolecule adaptor activity / protease binding ...death domain binding / endopeptidase complex / TP53 Regulates Transcription of Caspase Activators and Caspases / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of apoptotic signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / apoptotic signaling pathway / cellular response to mechanical stimulus / protein-macromolecule adaptor activity / protease binding / positive regulation of apoptotic process / DNA damage response / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain-containing protein CRADD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWu, H. / Park, H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of RAIDD Death Domain Implicates Potential Mechanism of PIDDosome Assembly
Authors: Park, H.H. / Wu, H.
History
DepositionDec 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death domain-containing protein CRADD


Theoretical massNumber of molelcules
Total (without water)13,2251
Polymers13,2251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.058, 56.058, 64.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Death domain-containing protein CRADD / Caspase and RIP adapter with death domain / RIP-associated protein with a death domain


Mass: 13224.930 Da / Num. of mol.: 1 / Fragment: Death Domain, residues 95-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRADD, RAIDD / Plasmid: pET 26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78560

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 1 ml of protein solution (4-6 mg/ml in 20 mM Tris at pH 8.0, 150 mM NaCl, mixed with 1 ml of a reservoir solution 2M Na/K phosphate at pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 8331 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.062

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / σ(F): 2 /
RfactorNum. reflection
Rfree0.241 -
Rwork0.231 -
obs-8331
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 0 0 704

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