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- PDB-1fio: CRYSTAL STRUCTURE OF YEAST T-SNARE PROTEIN SSO1 -

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Basic information

Entry
Database: PDB / ID: 1fio
TitleCRYSTAL STRUCTURE OF YEAST T-SNARE PROTEIN SSO1
ComponentsSSO1 PROTEIN
KeywordsMEMBRANE PROTEIN / four helix bundle / alpha helix
Function / homology
Function and homology information


vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / sporulation / Golgi vesicle fusion to target membrane / trans-Golgi Network Vesicle Budding / prospore membrane / ascospore formation / COPII-mediated vesicle transport / vesicle fusion ...vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / sporulation / Golgi vesicle fusion to target membrane / trans-Golgi Network Vesicle Budding / prospore membrane / ascospore formation / COPII-mediated vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / Golgi to plasma membrane transport / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / SNARE complex assembly / exocytosis / endomembrane system / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / cell periphery / intracellular protein transport / Golgi membrane / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / multiwavelength anomalous diffraction / Resolution: 2.1 Å
AuthorsMunson, M. / Chen, X. / Cocina, A.E. / Schultz, S.M. / Hughson, F.M.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Interactions within the yeast t-SNARE Sso1p that control SNARE complex assembly.
Authors: Munson, M. / Chen, X. / Cocina, A.E. / Schultz, S.M. / Hughson, F.M.
History
DepositionAug 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SSO1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9293
Polymers22,7981
Non-polymers1312
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.517, 49.855, 113.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SSO1 PROTEIN


Mass: 22798.424 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN
Source method: isolated from a genetically manipulated source
Details: YEAST T-SNARE PROTEIN
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PLM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32867
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.65 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, PEG 4000, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MHEPES1reservoir
314 %(w/v)PEG40001reservoir
410 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979345
DetectorType: BRANDEIS / Detector: CCD / Date: Mar 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979345 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. all: 18088 / Num. obs: 18088 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1797 / Rsym value: 0.38 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: multiwavelength anomalous diffraction
Resolution: 2.1→8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1398 10 %RANDOM
Rwork0.219 ---
all0.227 14265 --
obs0.221 14025 97.3 %-
Solvent computationSolvent model: flat model / Bsol: 80.7191 Å2 / ksol: 0.455486 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-8 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 2 153 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d16
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_mcbond_it4.831.5
X-RAY DIFFRACTIONc_mcangle_it6.642
X-RAY DIFFRACTIONc_scbond_it5.382
X-RAY DIFFRACTIONc_scangle_it8.852.5
LS refinement shellResolution: 2.1→2.17 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 126 9.2 %
Rwork0.238 1239 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.59

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