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Yorodumi- PDB-1nsf: D2 HEXAMERIZATION DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nsf | ||||||
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Title | D2 HEXAMERIZATION DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) | ||||||
Components | N-ETHYLMALEIMIDE SENSITIVE FACTOR | ||||||
Keywords | PROTEIN TRANSPORT / ENDOPLASMIC RETICULUM / GOLGI STACK / ATP-BINDING | ||||||
Function / homology | Function and homology information SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / intracellular protein transport / PDZ domain binding / potassium ion transport / positive regulation of protein catabolic process / midbody / protein-containing complex binding / protein kinase binding / 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 / MAD / Resolution: 1.9 Å | ||||||
Authors | Yu, R.C. / Hanson, P.I. / Jahn, R. / Brunger, A.T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP. Authors: Yu, R.C. / Hanson, P.I. / Jahn, R. / Brunger, A.T. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Domain Structure of an N-Ethylmaleimide-Sensitive Fusion Protein Involved in Vesicular Transport Authors: Tagaya, M. / Wilson, D.W. / Brunner, M. / Arango, N. / Rothman, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nsf.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nsf.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nsf_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 1nsf_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 1nsf_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1nsf_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/1nsf ftp://data.pdbj.org/pub/pdb/validation_reports/ns/1nsf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30486.451 Da / Num. of mol.: 1 / Fragment: D2 HEXAMERIZATION DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Cell line: CHO / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P18708 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.05 / Details: pH 6.05 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging dropDetails: drop contains equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Mar 1, 1998 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→500 Å / Num. obs: 50548 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.334 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→500 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1105949.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.69 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.333 / Rfactor obs: 0.288 |