+Open data
-Basic information
Entry | Database: PDB / ID: 1epu | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY crystal structure of neuronal SEC1 from squid | ||||||
Components | S-SEC1 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / PARALLEL BETA-SHEETS / LEFT-HAND TURN CONNECTION / HELICAL BUNDLE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Loligo pealei (longfin inshore squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / TWO-WAVELENGTH MAD / Resolution: 2.4 Å | ||||||
Authors | Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis. Authors: Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary X-ray Analysis of Squid Neuronal Sec1 Authors: Bracher, A. / Dresbach, T. / Betz, H. / Weissenhorn, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1epu.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1epu.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 1epu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epu ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epu | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 68815.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Cellular location: GIANT AXON / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O62547 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.77 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: batch crystallization / pH: 7.4 Details: Hepes, potassium chloride, dithiothreitol, pH 7.4, BATCH CRYSTALLIZATION, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging dropDetails: Bracher, A., (2000) Acta Crystallogr., Sect.D, 56, 501. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 34634 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 55.95 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4042 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 116511 |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: TWO-WAVELENGTH MAD / Resolution: 2.4→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.72 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.43 Å / Total num. of bins used: 30 /
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 29059 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|