+Open data
-Basic information
Entry | Database: PDB / ID: 1qcs | ||||||
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Title | N-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) | ||||||
Components | N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N) | ||||||
Keywords | FUSION PROTEIN / DOUBLE-PSI BETA BARREL ALPHA BETA ROLL | ||||||
Function / homology | Function and homology information SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport / positive regulation of protein catabolic process / midbody / protein-containing complex binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Yu, R.C. / Jahn, R. / Brunger, A.T. | ||||||
Citation | Journal: Mol.Cell / Year: 1999 Title: NSF N-terminal domain crystal structure: models of NSF function. Authors: Yu, R.C. / Jahn, R. / 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 | 1qcs.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qcs.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/1qcs ftp://data.pdbj.org/pub/pdb/validation_reports/qc/1qcs | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Is one domain of three in the NSF protomer. Biologically NSF is a hexamer. SYMMETRY OPERATORS AND RELEVANT TRANSLATIONS FOR HEXAMERIZATION ARE UNKNOWN. NSF CONTAINS 3 DOMAINS: N, D1, AND D2. D2 IS THE HEXAMERIZATION DOMAIN. BOTH THE SPATIAL ORIENTATION OF N RELATIVE TO D2, AND THE STRUCTURE OF IN THE INTERMEDIATE D1 DOMAIN ARE NOT KNOWN. |
-Components
#1: Protein | Mass: 23548.947 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF NSF Source method: isolated from a genetically manipulated source Details: THIS PROTEIN IS ONE DOMAIN OF THREE IN THE NSF PROTOMER. BIOLOGICALLY NSF IS A HEXAMER. Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: OVARY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Keywords: THIS PROTEIN IS ONE DOMAIN OF THREE IN THE NSF PROTOMER. BIOLOGICALLY NSF IS A HEXAMER. References: UniProt: P18708 | ||
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#2: Chemical | #3: 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: 2.38 Å3/Da / Density % sol: 48.21 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Vapor diffusion, hanging drop, 100 mM Tris pH 8.7, 2.0 M ammonium sulfate, 10 mM dithiothreitol (DTT), VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting 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: 0.9799, 0.9801, 0.9998, 0.9537 | |||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Feb 13, 1998 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 37996 / Num. obs: 32752 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.4 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.051 / Num. unique all: 3100 / % possible all: 92.7 | |||||||||||||||
Reflection | *PLUS Num. obs: 33216 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Resolution: 1.9→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2145257.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber Details: MLHL target function and density modified, combined phases used in refinements. Wavelength 3 (low energy remote, 0.9998 Angstrom) data used for refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.28 Å2 / ksol: 0.403 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / 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 Rfactor obs: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.53 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.97 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.24 / Total num. of bins used: 10 |