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- PDB-2fji: Crystal structure of the C-terminal domain of the exocyst subunit... -

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Basic information

Entry
Database: PDB / ID: 2fji
TitleCrystal structure of the C-terminal domain of the exocyst subunit Sec6p
ComponentsExocyst complex component SEC6
KeywordsENDOCYTOSIS/EXOCYTOSIS / Exocyst complex / exocytosis / tandem helical bundles / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


exocyst localization / negative regulation of SNARE complex assembly / exocyst / prospore membrane / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / exocytosis ...exocyst localization / negative regulation of SNARE complex assembly / exocyst / prospore membrane / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / exocytosis / SNARE binding / protein transport
Similarity search - Function
Exocyst complex component Sec6, C-terminal domain / Tetracycline Repressor; domain 2 - #50 / Exocyst complex component EXOC3/Sec6, C-terminal domain / Exocyst complex component EXOC3/Sec6 / Exocyst complex component Sec6 / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component SEC6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSivaram, M.V. / Munson, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: The structure of the exocyst subunit Sec6p defines a conserved architecture with diverse roles.
Authors: Sivaram, M.V. / Furgason, M.L. / Brewer, D.N. / Munson, M.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
1: Exocyst complex component SEC6
2: Exocyst complex component SEC6


Theoretical massNumber of molelcules
Total (without water)92,5012
Polymers92,5012
Non-polymers00
Water11,061614
1
1: Exocyst complex component SEC6


Theoretical massNumber of molelcules
Total (without water)46,2511
Polymers46,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2: Exocyst complex component SEC6


Theoretical massNumber of molelcules
Total (without water)46,2511
Polymers46,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.295, 63.301, 151.468
Angle α, β, γ (deg.)90.00, 103.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis domain is a monomer. There are 2 domains in the asymmetric unit (chains A & B)

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Components

#1: Protein Exocyst complex component SEC6


Mass: 46250.719 Da / Num. of mol.: 2 / Fragment: C-terminal domain Sec6CT2 (residues 411-805)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC6 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), BL21(DE3) RIL-X / References: UniProt: P32844
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2

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Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1%-4% PEG 6000, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9793, 0.9792, 0.9679
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 9, 2005
ADSC QUANTUM 3152CCDSep 15, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si(111) or (220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97921
30.96791
41.11
ReflectionRedundancy: 3.3 % / Number: 131541 / Rmerge(I) obs: 0.09 / Χ2: 4.203 / D res high: 2.3 Å / D res low: 50 Å / % possible obs: 76.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.265099.110.07815.8423.8
4.185.2699.410.0765.1533.7
3.654.1899.210.0884.1213.7
3.323.6598.210.12.4423.6
3.083.3297.510.1281.6893.5
2.93.0895.210.1611.2753.3
2.752.98610.1941.123.1
2.632.7573.310.221.1942.9
2.532.6360.310.2341.0242.7
2.442.5349.410.260.9662.3
2.372.4436.710.2680.9512.1
2.32.3726.510.2771.0931.8
ReflectionResolution: 2.4→50 Å / Num. all: 78684 / Num. obs: 76939 / % possible obs: 98.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Χ2: 1.131
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.421 / Num. unique all: 7817 / Χ2: 0.838 / % possible all: 98.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM acentric: 0.303 / FOM centric: 0.084 / Reflection acentric: 61378 / Reflection centric: 3312
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.520613783312
ANO_10.6202.520583310
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.82-2000824183
ISO_17.4-9.82001321185
ISO_16.19-7.4001690169
ISO_15.42-6.19001981159
ISO_14.89-5.42002230167
ISO_14.48-4.89002476171
ISO_14.17-4.48002673154
ISO_13.91-4.17002869147
ISO_13.69-3.91003054149
ISO_13.51-3.69003221158
ISO_13.35-3.51003404174
ISO_13.21-3.35003536179
ISO_13.09-3.21003667184
ISO_12.98-3.09003797181
ISO_12.88-2.98003962187
ISO_12.79-2.88004021178
ISO_12.71-2.79004181175
ISO_12.63-2.71004241159
ISO_12.56-2.63004185135
ISO_12.5-2.56004045118
ANO_19.82-200.52106880
ANO_17.4-9.820.496011830
ANO_16.19-7.40.474014980
ANO_15.42-6.190.492018830
ANO_14.89-5.420.542021640
ANO_14.48-4.890.59024350
ANO_14.17-4.480.6026360
ANO_13.91-4.170.647028360
ANO_13.69-3.910.704030280
ANO_13.51-3.690.758031910
ANO_13.35-3.510.804033370
ANO_13.21-3.350.863034430
ANO_13.09-3.210.895035310
ANO_12.98-3.090.925036300
ANO_12.88-2.980.957037910
ANO_12.79-2.880.973038270
ANO_12.71-2.790.986039290
ANO_12.63-2.711039620
ANO_12.56-2.631.004038020
ANO_12.5-2.561.008035370
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
163.92531.77465.66SE30.70.79
251.3139.70469.794SE21.20.71
340.81539.04860.384SE29.60.77
457.24961.64667.92SE260.65
589.7672.7317.212SE46.80.68
613.54957.0030.442SE48.40.7
7-14.54444.00360.894SE30.80.59
866.85961.07168.879SE460.6
938.70240.57866.043SE20.10.38
1085.3152.50941.781SE43.50.5
11-17.56440.7659.351SE57.70.65
1294.94624.65113.919SE35.60.58
1383.66832.19821.014SE35.60.45
1473.24247.21262.881SE14.30.27
1584.54455.98244.83SE600.71
1652.75522.78466.446SE23.20.4
17100.63523.9622.058SE45.30.42
1870.38949.56456.008SE42.70.41
1984.3523.65625.149SE600.62
2026.40244.43263.188SE47.90.4
2114.8126.76970.27SE600.47
2244.11842.61866.108SE600.5
2390.98541.43412.345SE36.20.3
2497.7925.28613.346SE600.36
252.00851.6359.035SE22.30.24
2696.10920.8945.507SE600.41
2788.42450.44338.723SE600.34
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.82-200.480.088824183
7.4-9.820.5180.0581321185
6.19-7.40.5590.1411690169
5.42-6.190.5670.1771981159
4.89-5.420.5170.1012230167
4.48-4.890.4930.1032476171
4.17-4.480.4760.0932673154
3.91-4.170.4550.0882869147
3.69-3.910.4140.0713054149
3.51-3.690.370.0733221158
3.35-3.510.3320.0673404174
3.21-3.350.2890.0773536179
3.09-3.210.2620.0543667184
2.98-3.090.2330.0663797181
2.88-2.980.2080.0643962187
2.79-2.880.1860.0814021178
2.71-2.790.1680.0684181175
2.63-2.710.1540.0694241159
2.56-2.630.1410.0764185135
2.5-2.560.1310.0794045118

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→15 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3870 5 %Random
Rwork0.249 ---
all-78171 --
obs-76939 98.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 62.9352 Å2 / ksol: 0.312866 e/Å3
Displacement parametersBiso max: 200.16 Å2 / Biso mean: 68.58 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1--4.94 Å20 Å222.67 Å2
2---20.59 Å20 Å2
3---25.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.52 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 0 614 6868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.4044875.10.39990400.0189726952798
2.51-2.640.3935035.20.35891260.0189725962999
2.64-2.80.3484554.70.31591730.0169675962899.5
2.8-3.020.3174684.80.2892870.0159768975599.9
3.02-3.320.2894714.80.25692800.0139762975199.9
3.32-3.790.30145850.27487570.0149757921594.4
3.79-4.750.26147950.21391440.0129818962398
4.75-150.2395495.60.20192620.0110005981198.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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