[English] 日本語
Yorodumi- PDB-3mp7: Lateral opening of a translocon upon entry of protein suggests th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mp7 | ||||||
---|---|---|---|---|---|---|---|
Title | Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / Membrane Protein Complex / Preprotein Translocase / Membrane Insertion / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP | ||||||
Function / homology | Function and homology information intracellular protein transmembrane transport / protein-transporting ATPase activity / protein secretion / protein targeting / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Egea, P.F. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. Authors: Egea, P.F. / Stroud, R.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mp7.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mp7.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mp7 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mp7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rh5S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53939.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: secY / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q8U019 |
---|---|
#2: Protein | Mass: 6944.483 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: secE / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q8TZK2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.4 % |
---|---|
Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG4000-PEG8000 15-25%, MES 100mM pH 6.2, Ca or Mg Acetate 50-200mM, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2008 | |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 23475 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 90.3 Å2 / Rsym value: 0.672 / Net I/σ(I): 9.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1RH5 Resolution: 2.9→49.43 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.793 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.69 Å2 / Biso mean: 78.672 Å2 / Biso min: 18.05 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.615 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.1 Å / Total num. of bins used: 8
|