+Open data
-Basic information
Entry | Database: PDB / ID: 1n5z | ||||||
---|---|---|---|---|---|---|---|
Title | Complex structure of Pex13p SH3 domain with a peptide of Pex14p | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / SH3 domain / PxxP motif | ||||||
Function / homology | Function and homology information Class I peroxisomal membrane protein import / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Peroxisomal protein import / peroxisomal membrane / protein transmembrane transporter activity / protein-macromolecule adaptor activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Douangamath, A. / Filipp, F.V. / Klein, A.T.J. / Barnett, P. / Zou, P. / Voorn-Brouwer, T. / Vega, M.C. / Mayans, O.M. / Sattler, M. / Distel, B. / Wilmanns, M. | ||||||
Citation | Journal: MOL.CELL / Year: 2002 Title: Topography for Independent Binding of alpha-Helical and PPII-Helical Ligands to a Peroxisomal SH3 Domain Authors: Douangamath, A. / Filipp, F.V. / Klein, A.T.J. / Barnett, P. / Zou, P. / Voorn-Brouwer, T. / Vega, M.C. / Mayans, O.M. / Sattler, M. / Distel, B. / Wilmanns, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n5z.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n5z.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 1n5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5z ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5z | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10782.284 Da / Num. of mol.: 2 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pMALc2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P80667 #2: Protein/peptide | Mass: 1695.914 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Chemically synthesized. This sequence occurs naturally in Saccharomyces cerevisiae. References: UniProt: P53112 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.2 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: Ammonium sulfate, lithium sulfate, tris, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2001 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 6298 / Num. obs: 5907 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.0065 / Net I/σ(I): 21.1 |
Reflection shell | Highest resolution: 2.7 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.033 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.33 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.558 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.36 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.974 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.234 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|