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- PDB-7v6e: DREP3 -

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Basic information

Entry
Database: PDB / ID: 7v6e
TitleDREP3
ComponentsDNAation factor-related protein 3, isoform A
KeywordsAPOPTOSIS / DREP3
Function / homologyCIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / regulation of apoptotic process / apoptotic process / DNAation factor-related protein 3, isoform A
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, S.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Helical filament structure of the DREP3 CIDE domain reveals a unified mechanism of CIDE-domain assembly.
Authors: Lee, S.Y. / Kwon, S. / Ha, H.J. / Lee, S.H. / Park, H.H.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAation factor-related protein 3, isoform A
B: DNAation factor-related protein 3, isoform A
C: DNAation factor-related protein 3, isoform A
D: DNAation factor-related protein 3, isoform A
E: DNAation factor-related protein 3, isoform A
F: DNAation factor-related protein 3, isoform A
G: DNAation factor-related protein 3, isoform A
H: DNAation factor-related protein 3, isoform A
I: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)87,5249
Polymers87,5249
Non-polymers00
Water00
1
A: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: DNAation factor-related protein 3, isoform A


Theoretical massNumber of molelcules
Total (without water)9,7251
Polymers9,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.460, 125.355, 168.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 117 through 154 or (resid 155...
d_3ens_1chain "C"
d_4ens_1(chain "D" and (resid 117 through 154 or (resid 155...
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1(chain "G" and (resid 117 through 154 or (resid 155...
d_8ens_1chain "H"
d_9ens_1(chain "I" and (resid 117 through 154 or (resid 155...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPROA1 - 77
d_21ens_1ASNPROB1 - 77
d_31ens_1ASNPROC1 - 77
d_41ens_1ASNPROD1 - 77
d_51ens_1ASNPROE1 - 77
d_61ens_1ASNPROF1 - 77
d_71ens_1ASNPROG1 - 77
d_81ens_1ASNPROH1 - 77
d_91ens_1ASNPROI1 - 77

NCS oper:
IDCodeMatrixVector
1given(-0.996647086386, 0.0817168976716, 0.00411507383215), (-0.0792456960769, -0.951545037202, -0.297123142534), (-0.0203643033516, -0.296453016195, 0.95483030133)24.4264306347, -57.8641336328, 50.1288309314
2given(-0.990142917767, 0.134458230032, -0.0392171744483), (-0.139469980462, -0.920838471168, 0.364149192731), (0.0128501729599, 0.366029362748, 0.93051457735)32.193061356, -69.4771353927, 49.3205022671
3given(0.998200297732, -0.0596056921764, -0.00658232991615), (-0.0429146397933, -0.786689469871, 0.61585551202), (-0.0418867437069, -0.614464677141, -0.787831619858)21.354332553, -74.485896941, -2.29696447618
4given(-0.999536819645, 0.0263815163071, -0.0151710833863), (0.00200357762453, 0.554477826497, 0.832196086028), (0.0303666239559, 0.831780232706, -0.554273860677)45.9508425553, -13.9484102723, 110.132961612
5given(0.997947579243, -0.0532531655045, 0.0355630348368), (-0.0442530740707, -0.17210701193, 0.984083757553), (-0.0462849275503, -0.983637777237, -0.174110392204)15.3061838826, -80.6414291255, -13.2164436611
6given(0.996550404966, 0.0147218215727, 0.0816734860956), (-0.0627334814809, 0.777914734088, 0.625230498929), (-0.054330476371, -0.628197369032, 0.776154794405)5.20189555621, -11.1906199842, 4.87169427923
7given(0.990635049075, -0.0269391418839, 0.133852464225), (-0.126489851123, 0.188021016093, 0.973985839256), (-0.0514054190466, -0.981795487941, 0.182852680458)10.630582088, -17.7517610219, 15.6574622863
8given(-0.98830434406, 0.094211219824, -0.119911507255), (-0.150170768509, -0.464527084268, 0.872733251496), (0.026519121369, 0.880533266856, 0.473241906599)39.3541402185, -78.2142903338, 56.9710835639

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Components

#1: Protein
DNAation factor-related protein 3, isoform A / DNAation factor-related protein 3 / isoform B / RH09855p


Mass: 9724.886 Da / Num. of mol.: 9 / Fragment: CIDE-N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Drep3, BcDNA:AT08574, CG13187, Dmel\CG8364, DREP-3, Drep-3, drep-3, DREP3, drep3, Rep3, CG8364, Dmel_CG8364
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0E9B7

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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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M citric acid pH 4.0, 0.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→42.11 Å / Num. obs: 45952 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 39.06 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.74
Reflection shellHighest resolution: 3 Å / Rmerge(I) obs: 0.053 / Num. unique obs: 2406

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2K

4d2k


Resolution: 3→42.11 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 3764 8.19 %
Rwork0.2054 42188 -
obs0.2092 45952 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.67 Å2
Refinement stepCycle: LAST / Resolution: 3→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 0 0 5622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01075721
X-RAY DIFFRACTIONf_angle_d1.22987723
X-RAY DIFFRACTIONf_chiral_restr0.0718864
X-RAY DIFFRACTIONf_plane_restr0.00951012
X-RAY DIFFRACTIONf_dihedral_angle_d5.51751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.08385665104
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.910089850883
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.05605466181
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.798254854969
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.918945470868
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.95493779048
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.04733254992
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.906186309587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.32041340.28871530X-RAY DIFFRACTION98.29
3.04-3.080.35781360.28131580X-RAY DIFFRACTION99.88
3.08-3.120.34591480.27231602X-RAY DIFFRACTION99.77
3.12-3.170.30161340.25051523X-RAY DIFFRACTION97.87
3.17-3.210.33361390.261564X-RAY DIFFRACTION99.94
3.21-3.260.31611380.25941562X-RAY DIFFRACTION100
3.26-3.320.27791400.26941602X-RAY DIFFRACTION98.92
3.32-3.370.33791360.24451520X-RAY DIFFRACTION99.46
3.37-3.430.32761390.23121589X-RAY DIFFRACTION100
3.43-3.50.29121440.21691596X-RAY DIFFRACTION99.89
3.5-3.570.32221360.20921532X-RAY DIFFRACTION98.93
3.57-3.650.29451350.22021534X-RAY DIFFRACTION100
3.65-3.730.25451420.20521612X-RAY DIFFRACTION99.83
3.73-3.830.31481390.22421560X-RAY DIFFRACTION99.3
3.83-3.930.26821390.21671548X-RAY DIFFRACTION100
3.93-4.050.24271470.19891615X-RAY DIFFRACTION99.55
4.05-4.180.19731330.16411523X-RAY DIFFRACTION100
4.18-4.330.19621460.17011611X-RAY DIFFRACTION99.94
4.33-4.50.17871390.16061513X-RAY DIFFRACTION99.64
4.5-4.70.1671420.14741591X-RAY DIFFRACTION99.88
4.7-4.950.17421420.15091563X-RAY DIFFRACTION99.94
4.95-5.260.20631390.16311571X-RAY DIFFRACTION99.88
5.26-5.670.21831420.17891572X-RAY DIFFRACTION99.94
5.67-6.240.22171460.21371565X-RAY DIFFRACTION99.94
6.24-7.130.24791410.20681559X-RAY DIFFRACTION99.77
7.13-8.970.25341350.19431563X-RAY DIFFRACTION99.88
8.98-42.110.2191330.21181488X-RAY DIFFRACTION94.3

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