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- PDB-2pfv: S. cerevisiae Exo70 with additional residues to 2.1 Angrstrom res... -

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Basic information

Entry
Database: PDB / ID: 2pfv
TitleS. cerevisiae Exo70 with additional residues to 2.1 Angrstrom resolution
ComponentsExocyst complex component EXO70Exocyst
KeywordsENDOCYTOSIS/EXOCYTOSIS / helix-turn-helix / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


exocyst assembly / exocyst localization / Insulin processing / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck ...exocyst assembly / exocyst localization / Insulin processing / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / exocytosis / Rho protein signal transduction / transport vesicle / phosphatidylinositol-4,5-bisphosphate binding / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
Tetracycline Repressor; domain 2 - #60 / 5 helical Cullin repeat like - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1150 / Exocyst complex component Exo70 / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / 5 helical Cullin repeat like / Cullin repeat-like-containing domain superfamily ...Tetracycline Repressor; domain 2 - #60 / 5 helical Cullin repeat like - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1150 / Exocyst complex component Exo70 / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / 5 helical Cullin repeat like / Cullin repeat-like-containing domain superfamily / Monooxygenase / 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 EXO70
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMoore, B.A. / Robinson, H.H. / Xu, Z.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The crystal structure of mouse Exo70 reveals unique features of the mammalian exocyst.
Authors: Moore, B.A. / Robinson, H.H. / Xu, Z.
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 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
A: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)64,6221
Polymers64,6221
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.541, 60.073, 222.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exocyst complex component EXO70 / Exocyst / Exocyst complex protein of 70 kDa


Mass: 64621.535 Da / Num. of mol.: 1 / Fragment: Residues 62-623
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EXO70 / Plasmid: pSJ7D / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P19658
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 278.15 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20.5% PEG 300, 0.2M lithium chloride, 0.1M glycine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 278.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2005 / Details: Vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 9.9 / Number: 222788 / Rmerge(I) obs: 0.086 / Χ2: 1.9 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 64253 / % possible obs: 95.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525099.510.0686.6176.5
3.594.5299.910.0643.0716.9
3.143.5910010.0771.9667.1
2.853.1410010.1091.2727.2
2.652.8510010.140.9637.1
2.492.6510010.1820.7776.9
2.372.4999.510.2230.6736.3
2.262.3794.610.2710.615.5
2.182.2685.610.3080.6634.9
2.12.187410.3570.5133.9
ReflectionResolution: 2.1→50 Å / Num. obs: 64253 / % possible obs: 95.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Χ2: 1.905 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.357 / Num. unique all: 2679 / Χ2: 0.513 / % possible all: 74

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.6 Å / D res low: 30 Å / FOM : 0.39 / Reflection: 18846
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
10.34823.874170.555SE39.31.42
229.76735.699205.458SE441.46
338.44728.295153.842SE38.81
432.55343.845154.566SE51.90.98
542.584.654210.526SE49.41
645.06555.515207.707SE601.07
733.93223.809148.551SE44.80.66
815.3529.607158.817SE19.80.33
932.30931.326214.476SE601.14
107.32138.387169.871SE34.70.43
113.40233.792170.944SE29.90.3
127.15257.28199.243SE12.90.21
1327.13752.098203.912SE600.47
Phasing MAD shell
Resolution (Å)FOM Reflection
9.19-300.351038
5.86-9.190.491636
4.6-5.860.452070
3.91-4.60.452424
3.45-3.910.432651
3.13-3.450.382884
2.88-3.130.323022
2.68-2.880.273121
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.63 / Reflection: 18846 / Reflection acentric: 16162 / Reflection centric: 2684
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-29.7670.910.940.86929595334
4.6-7.40.860.90.7226692129540
3.7-4.60.850.870.7432792761518
3.3-3.70.770.780.6432162813403
2.8-3.30.580.590.4755084915593
2.6-2.80.410.420.3332452949296

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.09phasing
CNS1.2refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→40.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 102660.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE FRIEDEL PAIRS WERE USED FOR phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2968 4.9 %RANDOM
Rwork0.237 ---
obs-60854 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.434 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.51 Å20 Å20 Å2
2--16.86 Å20 Å2
3----10.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 0 111 4415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 299 4.3 %
Rwork0.316 6617 -
obs-6916 60.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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