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- PDB-5xpb: Crystal Structure of Selenomethionine labelled Drep4 CIDE domain -

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Basic information

Entry
Database: PDB / ID: 5xpb
TitleCrystal Structure of Selenomethionine labelled Drep4 CIDE domain
ComponentsDNAation factor-related protein 4
KeywordsAPOPTOSIS / Energy metabolism / DNA Fragmentation Factor / drep4 / CIDE
Function / homology
Function and homology information


Apoptosis induced DNA fragmentation / DNA nuclease activity / apoptotic DNA fragmentation / nucleosome binding / DNA endonuclease activity / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
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 / Ubiquitin-like (UB roll) - #10 / His-Me finger superfamily / Ubiquitin-like (UB roll) ...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 / Ubiquitin-like (UB roll) - #10 / His-Me finger superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
DNAation factor-related protein 4
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.996 Å
AuthorsPark, H.H. / Jeong, J.H.
CitationJournal: To Be Published
Title: Crystal Structure of Selenomethionine labelled Drep4 CIDE domain
Authors: Park, H.H.
History
DepositionJun 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAation factor-related protein 4
B: DNAation factor-related protein 4
C: DNAation factor-related protein 4
D: DNAation factor-related protein 4
E: DNAation factor-related protein 4
F: DNAation factor-related protein 4
G: DNAation factor-related protein 4
H: DNAation factor-related protein 4
I: DNAation factor-related protein 4
J: DNAation factor-related protein 4


Theoretical massNumber of molelcules
Total (without water)113,57310
Polymers113,57310
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-24 kcal/mol
Surface area42660 Å2
Unit cell
Length a, b, c (Å)56.511, 103.722, 103.820
Angle α, β, γ (deg.)102.46, 105.81, 105.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNAation factor-related protein 4 / Drep4


Mass: 11357.307 Da / Num. of mol.: 10 / Fragment: CIDE (UNP RESIDUES 39-130)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Drep4, Drep-4, drep4, Rep4, CG9414, Dmel_CG9414 / Plasmid: pOKD / Details (production host): non-commmercial / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9V3H0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.71 Å3/Da / Density % sol: 77.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M tris-hydrochloride pH 8.5, 20 mM ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.996→30 Å / Num. obs: 38172 / % possible obs: 81.6 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.03
Reflection shellResolution: 2.996→3.103 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3334 / % possible all: 65

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHENIX1.9_1690data reduction
HKL-2000data scaling
PHENIX1.9_1690phasing
RefinementMethod to determine structure: SAD / Resolution: 2.996→29.83 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 30.8
RfactorNum. reflection% reflection
Rfree0.2634 1992 5.22 %
Rwork0.2164 --
obs0.2188 38148 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.996→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 0 2 6748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116886
X-RAY DIFFRACTIONf_angle_d1.3389297
X-RAY DIFFRACTIONf_dihedral_angle_d15.1494203
X-RAY DIFFRACTIONf_chiral_restr0.0751031
X-RAY DIFFRACTIONf_plane_restr0.0091200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9959-3.07080.40711130.42412222X-RAY DIFFRACTION78
3.0708-3.15370.4471400.41462366X-RAY DIFFRACTION84
3.1537-3.24640.42611390.37052451X-RAY DIFFRACTION88
3.2464-3.35110.37781300.33762498X-RAY DIFFRACTION87
3.3511-3.47070.3591340.31052468X-RAY DIFFRACTION90
3.4707-3.60940.35871320.27352540X-RAY DIFFRACTION90
3.6094-3.77340.31921450.24662648X-RAY DIFFRACTION93
3.7734-3.97190.25381520.20782655X-RAY DIFFRACTION94
3.9719-4.22010.2561480.18532605X-RAY DIFFRACTION94
4.2201-4.54490.18981530.14882730X-RAY DIFFRACTION96
4.5449-5.00030.15571570.13122746X-RAY DIFFRACTION98
5.0003-5.71940.26951470.17112775X-RAY DIFFRACTION98
5.7194-7.18920.21151490.18442757X-RAY DIFFRACTION98
7.1892-29.83130.20231530.15262695X-RAY DIFFRACTION96

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