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Basic information

Entry
Database: PDB / ID: 3onx
TitleCrystal structure of a domain of a protein involved in formation of actin cytoskeleton
ComponentsBud site selection protein 6
KeywordsPROTEIN BINDING / coiled-coil
Function / homology
Function and homology information


cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity ...cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / positive regulation of actin nucleation / astral microtubule organization / cell tip / incipient cellular bud site / cellular bud tip / cellular bud neck / mating projection tip / spindle pole body / establishment of cell polarity / actin filament bundle assembly / enzyme activator activity / regulation of actin cytoskeleton organization / regulation of protein localization / actin binding / cytoplasm
Similarity search - Function
Actin interacting protein 3, C-terminal domain / Actin interacting protein 3, C-terminal / Actin interacting protein 3-like, C-terminal / Actin interacting protein 3 / Actin interacting protein 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bud site selection protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.904 Å
AuthorsTu, D. / Eck, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the formin-interaction domain of the actin nucleation-promoting factor Bud6.
Authors: Tu, D. / Graziano, B.R. / Park, E. / Zheng, W. / Li, Y. / Goode, B.L. / Eck, M.J.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bud site selection protein 6
B: Bud site selection protein 6


Theoretical massNumber of molelcules
Total (without water)32,9922
Polymers32,9922
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-54 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.307, 67.424, 58.755
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bud site selection protein 6 / Actin-interacting protein 3


Mass: 16496.176 Da / Num. of mol.: 2 / Fragment: coiled-coil domain (unp residues 549-688)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: AIP3, BUD6, L8543.5, YLR319C / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P41697

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 9% PEG 3350, 85 mM sodium malonate (pH 7.0), 25% glycerol, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2008
RadiationMonochromator: MD2 microdiffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17136 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2 / Num. unique all: 1287 / % possible all: 71.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.904→35.028 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.7 / Phase error: 32.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1710 10.01 %random
Rwork0.2349 ---
obs0.239 17076 94.74 %-
all-17076 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.01 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.2393 Å20 Å224.9708 Å2
2--9.2955 Å2-0 Å2
3----15.5349 Å2
Refinement stepCycle: LAST / Resolution: 2.904→35.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 0 0 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012066
X-RAY DIFFRACTIONf_angle_d1.1892772
X-RAY DIFFRACTIONf_dihedral_angle_d22.092820
X-RAY DIFFRACTIONf_chiral_restr0.072320
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9037-2.98910.37731190.3522882X-RAY DIFFRACTION66
2.9891-3.08550.42921360.34861196X-RAY DIFFRACTION86
3.0855-3.19570.37091550.34361192X-RAY DIFFRACTION92
3.1957-3.32350.38041460.31691341X-RAY DIFFRACTION98
3.3235-3.47470.3361500.2851324X-RAY DIFFRACTION99
3.4747-3.65770.27641690.24221321X-RAY DIFFRACTION100
3.6577-3.88660.28611350.2081360X-RAY DIFFRACTION100
3.8866-4.18620.2581520.19561349X-RAY DIFFRACTION99
4.1862-4.60670.28431360.19021350X-RAY DIFFRACTION100
4.6067-5.27130.23911490.2021347X-RAY DIFFRACTION98
5.2713-6.63390.28021280.26411365X-RAY DIFFRACTION100
6.6339-35.03090.16591350.17681339X-RAY DIFFRACTION99

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