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- PDB-1qqe: CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17 -

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Basic information

Entry
Database: PDB / ID: 1qqe
TitleCRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17
ComponentsVESICULAR TRANSPORT PROTEIN SEC17
KeywordsPROTEIN TRANSPORT / HELIX-TURN-HELIX TPR-LIKE REPEAT
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / soluble NSF attachment protein activity / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / SNARE complex ...Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / soluble NSF attachment protein activity / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / SNARE complex / fungal-type vacuole membrane / syntaxin binding / ATPase activator activity / intracellular protein transport / autophagy / cytosol
Similarity search - Function
NSF attachment protein / Soluble NSF attachment protein, SNAP / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Alpha-soluble NSF attachment protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsRice, L.M. / Brunger, A.T.
CitationJournal: Mol.Cell / Year: 1999
Title: Crystal structure of the vesicular transport protein Sec17: implications for SNAP function in SNARE complex disassembly.
Authors: Rice, L.M. / Brunger, A.T.
History
DepositionJun 4, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VESICULAR TRANSPORT PROTEIN SEC17


Theoretical massNumber of molelcules
Total (without water)32,8251
Polymers32,8251
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.900, 107.900, 46.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is a monomer

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Components

#1: Protein VESICULAR TRANSPORT PROTEIN SEC17


Mass: 32824.734 Da / Num. of mol.: 1 / Mutation: M1I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.9
Details: POLYETHYLENEIMINE, SODIUM CITRATE, SODIUM CHLORIDE, GLYCEROL, DTT, pH 5.9, MICROBATCH, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
2100 mMsodium citrate1reservoir
3200 mM1reservoirNaCl
41.5-2. %polyethyleneimine1reservoir
53 %glycerol1reservoir
610 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 11997 / Num. obs: 11997 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 90.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.472 / % possible all: 99.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.3 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
CNS0.5refinement
ADSCdata collection
SCALEPACKdata scaling
CNS0.5phasing
RefinementResolution: 2.9→19.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1407425.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1098 9.5 %RANDOM
Rwork0.26 ---
all0.262 12007 --
obs0.262 11625 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.45 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.25 Å20 Å20 Å2
2---7.25 Å20 Å2
3---14.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 4 2220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 378 10.7 %
Rwork0.441 3144 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.5 % / Rfactor obs: 0.259 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 67.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg18.2
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.475 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.441 / Rfactor obs: 0.452

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