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- PDB-6a8w: Crystal structure of the FHA domain of Far9 -

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Basic information

Entry
Database: PDB / ID: 6a8w
TitleCrystal structure of the FHA domain of Far9
ComponentsVacuolar protein sorting-associated protein 64
KeywordsPROTEIN BINDING / FHA domain / phosphopeptide recognition / homolog of SLMAP
Function / homology
Function and homology information


re-entry into mitotic cell cycle after pheromone arrest / cellular response to pheromone / FAR/SIN/STRIPAK complex / protein targeting to vacuole / endoplasmic reticulum-Golgi intermediate compartment / TOR signaling / regulation of cell cycle / endoplasmic reticulum membrane / endoplasmic reticulum / cytoplasm
Similarity search - Function
: / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 64
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.844 Å
AuthorsChen, M. / Zhang, W.Q. / Zhou, Z.C.
CitationJournal: To be published
Title: Topological Structure and Dynamic Assembly of the STRIPAK Complex
Authors: Chen, M. / Zhou, Z.C.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 64


Theoretical massNumber of molelcules
Total (without water)15,6771
Polymers15,6771
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.991, 59.414, 64.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-400-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 64 / Factor arrest protein 9


Mass: 15677.396 Da / Num. of mol.: 1 / Fragment: UNP residues 160-295 / Mutation: L167M, T269M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS64, FAR9, YDR200C, YD9346.10C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: Q03944
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 6%(v/v) Tacsimate pH 6.0; 0.1M MES pH 6.0; 25%(w/v) polyethylene glycol 4,000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 11148 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 19.42 Å2 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.053 / Rrim(I) all: 0.193 / Net I/σ(I): 19.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 550 / CC1/2: 0.759 / Rpim(I) all: 0.403 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.844→29.707 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.92 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2227 2045 9.97 %
Rwork0.1905 --
obs0.1937 11126 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.844→29.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 118 1105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071001
X-RAY DIFFRACTIONf_angle_d0.8751349
X-RAY DIFFRACTIONf_dihedral_angle_d3.013613
X-RAY DIFFRACTIONf_chiral_restr0.063156
X-RAY DIFFRACTIONf_plane_restr0.004176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8443-1.88720.26841290.27391143X-RAY DIFFRACTION92
1.8872-1.93440.28071410.27281215X-RAY DIFFRACTION100
1.9344-1.98670.29111350.23991275X-RAY DIFFRACTION100
1.9867-2.04510.1961350.2091216X-RAY DIFFRACTION100
2.0451-2.11110.22451380.19551240X-RAY DIFFRACTION100
2.1111-2.18660.28111350.19281224X-RAY DIFFRACTION100
2.1866-2.27410.2321360.1931260X-RAY DIFFRACTION100
2.2741-2.37750.18351350.18121205X-RAY DIFFRACTION100
2.3775-2.50280.2521410.18491247X-RAY DIFFRACTION100
2.5028-2.65950.2631390.19881247X-RAY DIFFRACTION100
2.6595-2.86470.2281390.18591215X-RAY DIFFRACTION100
2.8647-3.15270.20521420.18561244X-RAY DIFFRACTION100
3.1527-3.60830.21891350.16651239X-RAY DIFFRACTION100
3.6083-4.54340.17871320.15731251X-RAY DIFFRACTION100
4.5434-29.71080.22591330.2031237X-RAY DIFFRACTION100

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