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- PDB-3i2w: Crystal structure of EFC/F-BAR domain of Drosophila Syndapin/PACSIN -

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Basic information

Entry
Database: PDB / ID: 3i2w
TitleCrystal structure of EFC/F-BAR domain of Drosophila Syndapin/PACSIN
ComponentsSyndapin
KeywordsENDOCYTOSIS / EFC / FBAR / SH3 domain
Function / homology
Function and homology information


cleavage furrow ingression / spindle assembly involved in male meiosis / male meiosis cytokinesis / subsynaptic reticulum / positive regulation of synaptic assembly at neuromuscular junction / neurotransmitter secretion / membrane organization / cleavage furrow / synaptic vesicle endocytosis / mitotic cytokinesis ...cleavage furrow ingression / spindle assembly involved in male meiosis / male meiosis cytokinesis / subsynaptic reticulum / positive regulation of synaptic assembly at neuromuscular junction / neurotransmitter secretion / membrane organization / cleavage furrow / synaptic vesicle endocytosis / mitotic cytokinesis / phospholipid binding / midbody / postsynaptic membrane / lipid binding / plasma membrane
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains ...Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.67 Å
AuthorsEdeling, M.A. / Owen, D.J. / Traub, L.M.
CitationJournal: Plos One / Year: 2009
Title: Structural requirements for PACSIN/Syndapin operation during zebrafish embryonic notochord development.
Authors: Edeling, M.A. / Sanker, S. / Shima, T. / Umasankar, P.K. / Honing, S. / Kim, H.Y. / Davidson, L.A. / Watkins, S.C. / Tsang, M. / Owen, D.J. / Traub, L.M.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Syndapin
B: Syndapin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3477
Polymers69,0942
Non-polymers2535
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-104 kcal/mol
Surface area29850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.595, 85.525, 192.860
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 Syndapin / LD46328p


Mass: 34547.016 Da / Num. of mol.: 2 / Fragment: EFC/F-BAR domain, UNP residues 14-303 out of 494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG33094, Dmel_CG33094, Synd, syndapin / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VDI1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 17% PEG 3350, 0.1M disodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.67→78.09 Å / Num. obs: 30043 / % possible obs: 99.5 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 22.2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4184 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.67→39.07 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.876 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.449 / ESU R Free: 0.286
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 1522 5.1 %RANDOM
Rwork0.23407 ---
obs0.2353 28462 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.65 Å2 / Biso mean: 43.032 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2---4.54 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.67→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 15 104 4731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9326345
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89125.328244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73415923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4611521
X-RAY DIFFRACTIONr_chiral_restr0.1360.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.52767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04824471
X-RAY DIFFRACTIONr_scbond_it3.46431953
X-RAY DIFFRACTIONr_scangle_it5.8774.51874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.675→2.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 106 -
Rwork0.344 2010 -
all-2116 -
obs--96.89 %

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