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- PDB-2fp3: Crystal structure of the Drosophila initiator caspase Dronc -

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Basic information

Entry
Database: PDB / ID: 2fp3
TitleCrystal structure of the Drosophila initiator caspase Dronc
ComponentsCaspase Nc
KeywordsHydrolysis/Apoptosis / caspase / apoptosis / initiator caspase activation / dimerization / active site conformation / Hydrolysis-Apoptosis COMPLEX
Function / homology
Function and homology information


hemocyte development / TP53 Regulates Transcription of Caspase Activators and Caspases / nurse cell apoptotic process / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / metamorphosis / compound eye development ...hemocyte development / TP53 Regulates Transcription of Caspase Activators and Caspases / nurse cell apoptotic process / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / metamorphosis / compound eye development / chaeta development / sperm individualization / apoptosome / programmed cell death involved in cell development / programmed necrotic cell death / CARD domain binding / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / programmed cell death / zymogen activation / dendrite morphogenesis / neuron remodeling / protein autoprocessing / ectopic germ cell programmed cell death / regulation of autophagy / central nervous system development / determination of adult lifespan / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of apoptotic process / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / apoptotic process / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...Rossmann fold - #1460 / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsYan, N. / Gu, L. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure and activation mechanism of the Drosophila initiator caspase dronc
Authors: Yan, N. / Huh, J.R. / Schirf, V. / Demeler, B. / Hay, B.A. / Shi, Y.
History
DepositionJan 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 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: Caspase Nc


Theoretical massNumber of molelcules
Total (without water)35,6091
Polymers35,6091
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.474, 162.474, 162.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Caspase Nc


Mass: 35609.320 Da / Num. of mol.: 1 / Fragment: Dronc residues 136-450 / Mutation: residue 284 cys-arg, residue 318 cys-ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Nc / Production host: Escherichia coli (E. coli)
References: UniProt: Q9XYF4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium mono-hydrogen phosphate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A111.1
SYNCHROTRONCHESS F220.9793, 0.9791, 0.964
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1synchrotron CHESS A-1SINGLE WAVELENGTHMx-ray1
2synchrotron CHESS-F2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97931
30.97911
40.9641
ReflectionResolution: 2.5→99 Å / Num. all: 12938 / Num. obs: 12899 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.5→2.6 Å / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 1326 random
Rwork0.222 --
all0.23 12906 -
obs0.23 12855 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 0 114 2133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_bond_d0.006

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