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- PDB-4d2k: Crystal structure of DREP2 CIDE domain -

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Basic information

Entry
Database: PDB / ID: 4d2k
TitleCrystal structure of DREP2 CIDE domain
ComponentsDREP2
KeywordsAPOPTOSIS / ENERGY METABOLISM / DNA FRAGMENTATION FACTOR (DFF)
Function / homology
Function and homology information


synaptic membrane / regulation of apoptotic process / postsynaptic membrane / apoptotic process / identical protein binding
Similarity search - Function
CIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
DNAation factor-related protein 2, isoform A / Drep2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsJang, T.H. / Park, H.H. / Kim, Y.G. / Jeong, J.H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: CIDE domains form functionally important higher-order assemblies for DNA fragmentation.
Authors: Choi, J.Y. / Qiao, Q. / Hong, S.H. / Kim, C.M. / Jeong, J.H. / Kim, Y.G. / Jung, Y.K. / Wu, H. / Park, H.H.
History
DepositionMay 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DREP2
B: DREP2
C: DREP2
D: DREP2


Theoretical massNumber of molelcules
Total (without water)40,2544
Polymers40,2544
Non-polymers00
Water66737
1
A: DREP2


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DREP2


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DREP2


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DREP2


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.283, 88.708, 113.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DREP2


Mass: 10063.541 Da / Num. of mol.: 4 / Fragment: CIDE DOMAIN, RESIDUES 1-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U787, UniProt: Q7K304*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.44 Å3/Da / Density % sol: 64.3 % / Description: NONE
Crystal growpH: 6.2
Details: 100 MM BIS-TRIS PH6.2, 300 MM MAGNESIUM FORMATE DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22067 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EEL

2eel


Resolution: 2.302→33.263 Å / SU ML: 0.29 / σ(F): 1.52 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1999 9.1 %
Rwork0.2165 --
obs0.2199 22067 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→33.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 37 2635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092645
X-RAY DIFFRACTIONf_angle_d1.3813574
X-RAY DIFFRACTIONf_dihedral_angle_d14.091004
X-RAY DIFFRACTIONf_chiral_restr0.057397
X-RAY DIFFRACTIONf_plane_restr0.008457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3018-2.35940.30141370.27851373X-RAY DIFFRACTION94
2.3594-2.42310.32341460.26961476X-RAY DIFFRACTION99
2.4231-2.49440.28231460.25311460X-RAY DIFFRACTION100
2.4944-2.57490.28021490.25141485X-RAY DIFFRACTION100
2.5749-2.66690.31261460.2591473X-RAY DIFFRACTION99
2.6669-2.77360.30451490.25511493X-RAY DIFFRACTION100
2.7736-2.89980.30081450.25481455X-RAY DIFFRACTION100
2.8998-3.05260.28561490.2531497X-RAY DIFFRACTION100
3.0526-3.24370.26831490.25451495X-RAY DIFFRACTION100
3.2437-3.49390.29571480.24561488X-RAY DIFFRACTION99
3.4939-3.8450.2962840.2298836X-RAY DIFFRACTION55
3.845-4.40030.22961370.18771378X-RAY DIFFRACTION90
4.4003-5.53980.21121540.16251547X-RAY DIFFRACTION100
5.5398-33.26610.20331600.19021612X-RAY DIFFRACTION99

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