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- PDB-3qwy: CED-2 -

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Basic information

Entry
Database: PDB / ID: 3qwy
TitleCED-2
ComponentsCell death abnormality protein 2
KeywordsSIGNALING PROTEIN / Cell Engulfment
Function / homology
Function and homology information


positive regulation of distal tip cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / positive regulation of engulfment of apoptotic cell / engulfment of apoptotic cell / apoptotic process involved in development / programmed cell death ...positive regulation of distal tip cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / positive regulation of engulfment of apoptotic cell / engulfment of apoptotic cell / apoptotic process involved in development / programmed cell death / enzyme-linked receptor protein signaling pathway / signaling adaptor activity / receptor tyrosine kinase binding / cell migration / actin cytoskeleton organization / protein-containing complex binding / apoptotic process / signal transduction / plasma membrane / cytoplasm
Similarity search - Function
: / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. ...: / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cell death abnormality protein 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsKang, Y. / Sun, J. / Liu, Y. / Sun, D. / Hu, Y. / Liu, Y.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of the cell corpse engulfment protein CED-2 in Caenorhabditis elegans.
Authors: Kang, Y. / Xu, J. / Liu, Y. / Sun, J. / Sun, D. / Hu, Y. / Liu, Y.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell death abnormality protein 2
B: Cell death abnormality protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1444
Polymers67,9562
Non-polymers1882
Water2,306128
1
A: Cell death abnormality protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0742
Polymers33,9781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell death abnormality protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0702
Polymers33,9781
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.211, 97.152, 71.096
Angle α, β, γ (deg.)90.00, 127.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-281-

HOH

21A-321-

HOH

31A-333-

HOH

41A-356-

HOH

51B-281-

HOH

61B-302-

HOH

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Components

#1: Protein Cell death abnormality protein 2 / Cell-corpse engulfment protein CED-2


Mass: 33978.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-2, Y41D4B.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NHC3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→63.5 Å / Num. obs: 18916

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→48.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.816 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 965 5.1 %RANDOM
Rwork0.20373 ---
obs0.20703 17951 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-1.62 Å2
2---0.14 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.52→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 11 128 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0222765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8231.9613744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5625338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33223.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71415457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.841520
X-RAY DIFFRACTIONr_chiral_restr0.1810.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.21108
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.21821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5741.51760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55522713
X-RAY DIFFRACTIONr_scbond_it4.04231184
X-RAY DIFFRACTIONr_scangle_it6.3074.51031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 49 -
Rwork0.39 1059 -
obs--78.86 %

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