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- PDB-1v0d: Crystal Structure of Caspase-activated DNase (CAD) -

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Basic information

Entry
Database: PDB / ID: 1v0d
TitleCrystal Structure of Caspase-activated DNase (CAD)
ComponentsDNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
KeywordsHYDROLASE / NUCLEASE / CASPASE-ACTIVATED DNASE
Function / homology
Function and homology information


Apoptosis induced DNA fragmentation / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / nuclease activity / DNA endonuclease activity / disordered domain specific binding / chromatin ...Apoptosis induced DNA fragmentation / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / nuclease activity / DNA endonuclease activity / disordered domain specific binding / chromatin / nucleolus / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #170 / DNA fragmentation factor 40, C-terminal / DNA fragmentation factor 40 / DNA fragmentation factor 40 kDa / CIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / His-Me finger superfamily / Helix Hairpins ...Helix Hairpins - #170 / DNA fragmentation factor 40, C-terminal / DNA fragmentation factor 40 / DNA fragmentation factor 40 kDa / CIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / His-Me finger superfamily / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
LEAD (II) ION / DNA fragmentation factor subunit beta
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWoo, E.-J. / Kim, Y.-G. / Kim, M.-S. / Han, W.-D. / Shin, S. / Oh, B.-H.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural Mechanism for Inactivation and Activation of Cad/Dff40 in the Apoptotic Pathway
Authors: Woo, E.-J. / Kim, Y.-G. / Kim, M.-S. / Han, W.-D. / Shin, S. / Robinson, H. / Park, S.-Y. / Oh, B.-H.
History
DepositionMar 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8984
Polymers37,6011
Non-polymers2973
Water28816
1
A: DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
hetero molecules

A: DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7958
Polymers75,2012
Non-polymers5946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.189, 110.189, 73.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT / DFF-40 / CASPASE-ACTIVATED DEOXYRIBONUCLEASE / CASPASE-ACTIVATED DNASECAD


Mass: 37600.664 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O54788
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9479
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9479 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 14995 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.246 -5 %
Rwork0.218 --
obs0.218 14995 94.8 %
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 3 16 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3894
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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