+Open data
-Basic information
Entry | Database: PDB / ID: 1ifq | ||||||
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Title | Sec22b N-terminal domain | ||||||
Components | vesicle trafficking protein Sec22bVesicle (biology and chemistry) | ||||||
Keywords | PROTEIN TRANSPORT / FIVE-STRANDED ANTI-PARALLEL BETA SHEET / ALPHA/BETA 3-LAYER SANDWICH | ||||||
Function / homology | Function and homology information Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / ER-Phagosome pathway ...Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / ER-Phagosome pathway / syntaxin binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / melanosome / synaptic vesicle / protein transport / Golgi membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Gonzalez Jr., L.C. / Weis, W.I. / Scheller, R.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: A novel snare N-terminal domain revealed by the crystal structure of Sec22b. Authors: Gonzalez Jr., L.C. / Weis, W.I. / Scheller, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifq.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifq.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ifq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifq ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16019.801 Da / Num. of mol.: 2 / Fragment: N-Terminal Domain (residues 2-127) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O08547 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: PEG 1000, ammonium sulfate, sodium citrate, glycerol, beta-mercaptoethanol, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: drop contains protein and reservoir solution in a 1:1 ratio | |||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 0.92537, 0.97929, 0.97945 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 21501 / Num. obs: 21210 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 50.3 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 24 / Limit k min: 0 / Limit l max: 42 / Limit l min: -43 / Observed criterion F max: 2462169.67 / Observed criterion F min: 1.715 / Rmerge(I) obs: 0.036 / Net I/σ(I): 31.2 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5.3 / % possible all: 90.9 | ||||||||||||
Reflection shell | *PLUS % possible obs: 90.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / 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: CNS bulk solvent model used / Bsol: 57.9904 Å2 / ksol: 0.357432 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.13 Å2 / Biso mean: 57.1 Å2 / Biso min: 30.71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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