+Open data
-Basic information
Entry | Database: PDB / ID: 1qqe | ||||||
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Title | CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17 | ||||||
Components | VESICULAR TRANSPORT PROTEIN SEC17 | ||||||
Keywords | PROTEIN TRANSPORT / HELIX-TURN-HELIX TPR-LIKE REPEAT | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / soluble NSF attachment protein activity / Intra-Golgi traffic / SNARE complex disassembly / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex ...Retrograde transport at the Trans-Golgi-Network / soluble NSF attachment protein activity / Intra-Golgi traffic / SNARE complex disassembly / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex / fungal-type vacuole membrane / vacuolar membrane / syntaxin binding / extrinsic component of membrane / ATPase activator activity / intracellular protein transport / autophagy / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Rice, L.M. / Brunger, A.T. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qqe.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqe.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqe ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.91 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Resolution: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.45 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.475 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.441 / Rfactor obs: 0.452 |