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- PDB-2a2f: Crystal Structure of Sec15 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2a2f
TitleCrystal Structure of Sec15 C-terminal domain
ComponentsExocyst complex component Sec15
KeywordsPROTEIN TRANSPORT / all helical structure
Function / homology
Function and homology information


Insulin processing / VxPx cargo-targeting to cilium / vesicle tethering involved in exocytosis / rhabdomere / exocyst / phototaxis / border follicle cell migration / chaeta development / Golgi to plasma membrane transport / endocytic recycling ...Insulin processing / VxPx cargo-targeting to cilium / vesicle tethering involved in exocytosis / rhabdomere / exocyst / phototaxis / border follicle cell migration / chaeta development / Golgi to plasma membrane transport / endocytic recycling / exocytosis / axon terminus / vesicle-mediated transport / axon guidance / protein localization to plasma membrane / intracellular protein transport / recycling endosome / small GTPase binding / cytoplasmic vesicle / endosome
Similarity search - Function
Exocyst complex subunit Sec15 C-terminal domain, N-terminal subdomain / Dsl1p vesicle tethering complex, Tip20p subunit, domain D / Exocyst complex component EXOC6/Sec15 / Exocyst complex component EXOC6/Sec15, C-terminal, domain 1 / Exocyst complex subunit Sec15, C-terminal / : / Exocyst complex subunit Sec15 C-terminal / Exocyst complex component EXOC6/Sec15, N-terminal / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Tetracycline Repressor; domain 2 ...Exocyst complex subunit Sec15 C-terminal domain, N-terminal subdomain / Dsl1p vesicle tethering complex, Tip20p subunit, domain D / Exocyst complex component EXOC6/Sec15 / Exocyst complex component EXOC6/Sec15, C-terminal, domain 1 / Exocyst complex subunit Sec15, C-terminal / : / Exocyst complex subunit Sec15 C-terminal / Exocyst complex component EXOC6/Sec15, N-terminal / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Tetracycline Repressor; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component 6
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWu, S. / Mehta, S.Q. / Pichaud, F. / Bellen, H.J. / Quiocho, F.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Sec15 interacts with Rab11 via a novel domain and affects Rab11 localization in vivo.
Authors: Wu, S. / Mehta, S.Q. / Pichaud, F. / Bellen, H.J. / Quiocho, F.A.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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
X: Exocyst complex component Sec15


Theoretical massNumber of molelcules
Total (without water)37,9621
Polymers37,9621
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Exocyst complex component Sec15

X: Exocyst complex component Sec15


Theoretical massNumber of molelcules
Total (without water)75,9232
Polymers75,9232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area2860 Å2
ΔGint-27 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.5, 93.9, 123.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Exocyst complex component Sec15


Mass: 37961.695 Da / Num. of mol.: 1 / Fragment: Sec15 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sec15 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9VDE6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium Citrate, ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97958,0.97949,0.96308
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2003 / Details: KOHZU: Double Crystal Si(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)MADMx-ray1
2Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979581
20.979491
30.963081
ReflectionResolution: 2.5→500 Å / Num. all: 16552 / Num. obs: 15141 / % possible obs: 91.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 80.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→500 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 740 random
Rwork0.243 --
all-16552 -
obs-15141 -
Refinement stepCycle: LAST / Resolution: 2.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 0 87 2511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.26

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