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- PDB-3sir: Crystal Structure of drICE -

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Basic information

Entry
Database: PDB / ID: 3sir
TitleCrystal Structure of drICE
ComponentsCaspase
KeywordsHYDROLASE / caspase
Function / homology
Function and homology information


: / BIR domain binding / Apoptotic cleavage of cellular proteins / negative regulation of Toll signaling pathway / nurse cell apoptotic process / SMAC, XIAP-regulated apoptotic response / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / negative regulation of peptidoglycan recognition protein signaling pathway / spermatid differentiation ...: / BIR domain binding / Apoptotic cleavage of cellular proteins / negative regulation of Toll signaling pathway / nurse cell apoptotic process / SMAC, XIAP-regulated apoptotic response / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / negative regulation of peptidoglycan recognition protein signaling pathway / spermatid differentiation / programmed cell death involved in cell development / programmed cell death / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / neuron remodeling / response to X-ray / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / proteolysis / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / 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 ...Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsLi, X. / Wang, J. / Shi, Y.
CitationJournal: Nat Commun / Year: 2011
Title: Structural mechanisms of DIAP1 auto-inhibition and DIAP1-mediated inhibition of drICE.
Authors: Li, X. / Wang, J. / Shi, Y.
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Caspase
B: Caspase
C: Caspase
D: Caspase


Theoretical massNumber of molelcules
Total (without water)118,1824
Polymers118,1824
Non-polymers00
Water543
1
A: Caspase
B: Caspase


Theoretical massNumber of molelcules
Total (without water)59,0912
Polymers59,0912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-24 kcal/mol
Surface area18350 Å2
MethodPISA
2
C: Caspase
D: Caspase


Theoretical massNumber of molelcules
Total (without water)59,0912
Polymers59,0912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-18 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.025, 56.025, 287.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Caspase / drICE / Caspase subunit p21 / Caspase subunit p12


Mass: 29545.594 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 78-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
References: UniProt: O01382, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALGS IS A COVALENT PEPTIDE FOR BINDING OF BIR1 MOLECULAR

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M Acetate pH4.4, 1.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.294
11-H, H+K, -L20.213
11K, H, -L30.214
11-h,-k,l40.279
ReflectionResolution: 2.68→50 Å / Num. obs: 27960 / % possible obs: 98.6 % / Observed criterion σ(F): 13.4 / Observed criterion σ(I): 2.2

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I3O

1i3o


Resolution: 2.68→45.97 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.87 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23517 1400 5 %RANDOM
Rwork0.16508 ---
obs0.1684 26529 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.349 Å2
Baniso -1Baniso -2Baniso -3
1--14.79 Å20 Å20 Å2
2---14.79 Å20 Å2
3---29.58 Å2
Refinement stepCycle: LAST / Resolution: 2.68→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 0 3 5766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0225873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7141.9397925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.7095695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08823.164275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.652151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6671542
X-RAY DIFFRACTIONr_chiral_restr0.0560.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024340
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2631.53559
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36725738
X-RAY DIFFRACTIONr_scbond_it3.66632314
X-RAY DIFFRACTIONr_scangle_it5.6834.52187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.218 1863 -
obs--89.91 %

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