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- PDB-1few: CRYSTAL STRUCTURE OF SMAC/DIABLO -

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Basic information

Entry
Database: PDB / ID: 1few
TitleCRYSTAL STRUCTURE OF SMAC/DIABLO
ComponentsSECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASESDiablo homolog
KeywordsAPOPTOSIS / Smac / DIABLO / caspase activation / IAP inhibition
Function / homology
Function and homology information


activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway ...activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron apoptotic process / positive regulation of apoptotic process / apoptotic process / mitochondrion / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChai, J. / Shi, Y.
CitationJournal: Nature / Year: 2000
Title: Structural and biochemical basis of apoptotic activation by Smac/DIABLO.
Authors: Chai, J. / Du, C. / Wu, J.W. / Kyin, S. / Wang, X. / Shi, Y.
History
DepositionJul 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES


Theoretical massNumber of molelcules
Total (without water)20,7591
Polymers20,7591
Non-polymers00
Water0
1
A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES

A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES


Theoretical massNumber of molelcules
Total (without water)41,5182
Polymers41,5182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area20320 Å2
MethodPISA
2
A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES

A: SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES


Theoretical massNumber of molelcules
Total (without water)41,5182
Polymers41,5182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2000 Å2
ΔGint-21 kcal/mol
Surface area20530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.5, 108.5, 70.4
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASES / Diablo homolog


Mass: 20759.084 Da / Num. of mol.: 1 / Fragment: SMAC/DIABLO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR28

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Dioxane, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %(v/v)1,4-dioxane1reservoir
3200 mMammonium sulfate1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. all: 12907 / Num. obs: 12842 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.242 / Num. unique all: 1219 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 97019
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 2.2→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 622 -random
Rwork0.245 ---
all0.25 12831 --
obs0.247 11728 91.4 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 0 0 1373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.012
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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