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- PDB-3bw6: Crystal structure of the longin domain of yeast Ykt6 -

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Basic information

Entry
Database: PDB / ID: 3bw6
TitleCrystal structure of the longin domain of yeast Ykt6
ComponentsSynaptobrevin homolog YKT6
KeywordsTRANSFERASE / Ykt6p / farnesylation / vacuole fusion / SNARE / Coiled coil / Lipoprotein / Membrane / Phosphoprotein / Prenylation
Function / homology
Function and homology information


amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity ...amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity / vesicle fusion / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / fungal-type vacuole / vacuolar membrane / autophagosome membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / intracellular protein transport / endosome membrane / endosome / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain ...YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Synaptobrevin homolog YKT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPylypenko, O. / Schonichen, A. / Ludwig, D. / Ungermann, C. / Goody, R.S. / Rak, A. / Geyer, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Farnesylation of the SNARE protein Ykt6 increases its stability and helical folding.
Authors: Pylypenko, O. / Schonichen, A. / Ludwig, D. / Ungermann, C. / Goody, R.S. / Rak, A. / Geyer, M.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptobrevin homolog YKT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2812
Polymers16,1851
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 78.890, 64.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Synaptobrevin homolog YKT6


Mass: 16185.141 Da / Num. of mol.: 1 / Fragment: Longin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKT6 / Production host: Escherichia coli (E. coli)
References: UniProt: P36015, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 3350, 150 mM ammonium sulphate, 100 mM MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 8335 / Num. obs: 8293 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.55 Å / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 415 random
Rwork0.24 --
all0.24 8335 -
obs0.24 8293 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 5 44 1145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008531
X-RAY DIFFRACTIONc_angle_deg1.27856

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