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- PDB-1ibx: NMR STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ibx
TitleNMR STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN COMPLEX
Components
  • CHIMERA OF IGG BINDING PROTEIN G AND DNA FRAGMENTATION FACTOR 45
  • DNA FRAGMENTATION FACTOR 40
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DFF40 / DFF45 / protein-protein complex / CIDE / CIDE domain complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of deoxyribonuclease activity / deoxyribonuclease inhibitor activity / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / chromatin => GO:0000785 / negative regulation of execution phase of apoptosis / Apoptosis induced DNA fragmentation ...negative regulation of deoxyribonuclease activity / deoxyribonuclease inhibitor activity / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / chromatin => GO:0000785 / negative regulation of execution phase of apoptosis / Apoptosis induced DNA fragmentation / DNA catabolic process / IgG binding / thymocyte apoptotic process / chaperone-mediated protein folding / protein folding chaperone / disordered domain specific binding / positive regulation of apoptotic process / protein domain specific binding / chromatin / nucleolus / enzyme binding / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
DNA fragmentation factor 45kDa, middle domain / DNA fragmentation factor 45 / DNA fragmentation factor 45kDa, C-terminal / DNA Fragmentation factor 45kDa, C terminal domain / 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. ...DNA fragmentation factor 45kDa, middle domain / DNA fragmentation factor 45 / DNA fragmentation factor 45kDa, C-terminal / DNA Fragmentation factor 45kDa, C terminal domain / 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 / IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA fragmentation factor subunit alpha / DNA fragmentation factor subunit beta / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsZhou, P. / Lugovskoy, A.A. / McCarty, J.S. / Li, P. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45.
Authors: Zhou, P. / Lugovskoy, A.A. / McCarty, J.S. / Li, P. / Wagner, G.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE "His A 81" in DFF40 is the first residue of a C-terminal His6 tag. All other five His ...SEQUENCE "His A 81" in DFF40 is the first residue of a C-terminal His6 tag. All other five His residues are not observable in the experiment. Chain B, is produced as a chimeric protein containing protein G B1 domain (-44 to 11) and DFF45 (12 to 100). The sequence for protein G B1 can also be found in PDB entry 1GB1 as residues 1 to 56. The engineered mutation when using PDB entry 1GB1 numbering, is T2Q.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA FRAGMENTATION FACTOR 40
B: CHIMERA OF IGG BINDING PROTEIN G AND DNA FRAGMENTATION FACTOR 45


Theoretical massNumber of molelcules
Total (without water)25,9952
Polymers25,9952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the least restraint violations
RepresentativeModel #10closest to the average

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Components

#1: Protein DNA FRAGMENTATION FACTOR 40 / DFF40 / CASPASE-ACTIVATED DNASE / CASPASE-ACTIVATED NUCLEASE


Mass: 9894.394 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (CIDE DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DFF40 / Plasmid: PET-30A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O76075, Hydrolases
#2: Protein CHIMERA OF IGG BINDING PROTEIN G AND DNA FRAGMENTATION FACTOR 45 / DFF45 / INHIBITOR OF CAD


Mass: 16100.919 Da / Num. of mol.: 1
Fragment: B1 DOMAIN OF PROTEIN G FUSED WITH N-TERMINAL DOMAIN (CIDE DOMAIN) OF DFF45
Mutation: T(-43)Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp., Homo sapiens / Genus: Streptococcus, Homo / Species: , / Strain: , / Gene: DFF45 / Plasmid: PET-30A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P19909, GenBank: 2065561, UniProt: O00273*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
9113D 13C-separated NOESY
10213D 13C-separated NOESY
3313D 15N-separated NOESY
4413D 15N-separated NOESY
5512D NOESY
6612D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Chain B, is produced as a chimeric protein containing protein G B1 domain (-44 to 11) and DFF45 (12 to 100). The residues ...Text: The structure was determined using triple-resonance NMR spectroscopy. Chain B, is produced as a chimeric protein containing protein G B1 domain (-44 to 11) and DFF45 (12 to 100). The residues of the Protein G B1 domain are used as a solubility enhancement tag to improve solubility and stability of target protein. These residues are not included in the structural calculation, thus the coordinates are not deposited.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM DFF40/DFF45 NTD complex 90% deuterated, U-15N/13C labeled DFF40 non-labeled DFF4520 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
20.6 mM DFF40/DFF45 NTD complex 90% deuterated, U-15N/13C labeled DFF45 non-labeled DFF4020 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
30.6 mM DFF40/DFF45 NTD complex U-15N labeled DFF40 non-labeled DFF4520 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
40.6 mM DFF40/DFF45 NTD complex U-15N labeled DFF45 non-labeled DFF4020 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
50.6 mM DFF40/DFF45 NTD complex perdeuterated, U-15N labeled DFF40 non-labeled DFF4520 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
60.6 mM DFF40/DFF45 NTD complex perdeuterated, U-15N labeled DFF45 non-labeled DFF4020 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
70.6 mM DFF40/DFF45 NTD complex 10% 13C labeled DFF40 non-labeled DFF4520 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
80.6 mM DFF40/DFF45 NTD complex 10% 13C labeled DFF45 non-labeled DFF4020 mM Phosphate buffer 5 mM DTT, 50 mM NaCl 10%D2O/90%H2O
90.6 mM DFF40/DFF45 NTD complex U-13C labeled DFF40 non-labeled DFF4520 mM Phosphate buffer 5 mM DTT, 50 mM NaCl D2O
100.6 mM DFF40/DFF45 NTD complex U-13C labeled DFF45 non-labeled DFF4020 mM Phosphate buffer 5 mM DTT, 50 mM NaCl D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulation, Inc.processing
XEASYv1.3Ch. Bartels et. al.data analysis
DYANAv1.5Guntert et al.structure solution
X-PLORv3.8Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 10

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