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- PDB-4mac: Crystal structure of CIDE-N domain of FSP27 -

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Basic information

Entry
Database: PDB / ID: 4mac
TitleCrystal structure of CIDE-N domain of FSP27
ComponentsCell death activator CIDE-3
KeywordsAPOPTOSIS / roll fold / Protein interaction / Perilipin1
Function / homology
Function and homology information


Lipid particle organization / lipid droplet fusion / lipid transfer activity / negative regulation of triglyceride metabolic process / phosphatidic acid binding / lipid storage / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process / lipid droplet ...Lipid particle organization / lipid droplet fusion / lipid transfer activity / negative regulation of triglyceride metabolic process / phosphatidic acid binding / lipid storage / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process / lipid droplet / phosphatidylinositol binding / molecular condensate scaffold activity / apoptotic process / endoplasmic reticulum / nucleus / cytosol
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
Lipid transferase CIDEC
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, H.H. / Lee, S.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Molecular basis for homo-dimerization of the CIDE domain revealed by the crystal structure of the CIDE-N domain of FSP27
Authors: Lee, S.M. / Jang, T.H. / Park, H.H.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell death activator CIDE-3
B: Cell death activator CIDE-3


Theoretical massNumber of molelcules
Total (without water)22,5482
Polymers22,5482
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell death activator CIDE-3


Theoretical massNumber of molelcules
Total (without water)11,2741
Polymers11,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cell death activator CIDE-3


Theoretical massNumber of molelcules
Total (without water)11,2741
Polymers11,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.354, 63.354, 37.606
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Cell death activator CIDE-3 / Cell death-inducing DFFA-like effector protein C / Fat-specific protein FSP27


Mass: 11274.087 Da / Num. of mol.: 2 / Fragment: UNP residues 32-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cidec, Fsp27 / Production host: Escherichia coli (E. coli) / References: UniProt: P56198
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 28% PEG1500, MMT buffer/NaOH, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2013
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→31.68 Å / Num. all: 11299 / Num. obs: 57364 / % possible obs: 40 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.1 Å / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.18 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29271 544 4.8 %RANDOM
Rwork0.22141 ---
obs0.22478 10752 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 0 73 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221309
X-RAY DIFFRACTIONr_angle_refined_deg1.9722.0021758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.10724.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.648159
X-RAY DIFFRACTIONr_chiral_restr0.1570.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021935
X-RAY DIFFRACTIONr_mcbond_it1.0361.5801
X-RAY DIFFRACTIONr_mcangle_it1.99721300
X-RAY DIFFRACTIONr_scbond_it3.4943508
X-RAY DIFFRACTIONr_scangle_it5.7264.5458
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 52 -
Rwork0.234 768 -
obs--98.2 %

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