+Open data
-Basic information
Entry | Database: PDB / ID: 1gyb | ||||||
---|---|---|---|---|---|---|---|
Title | N77Y point mutant of yNTF2 bound to FxFG nucleoporin repeat | ||||||
Components |
| ||||||
Keywords | NUCLEAR TRANSPORT | ||||||
Function / homology | Function and homology information nuclear pore central transport channel / nucleocytoplasmic transport / nuclear import signal receptor activity / small GTPase binding / protein import into nucleus / nuclear envelope / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bayliss, R. / Stewart, M. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Structural Basis for the Interaction between Ntf2 and Nucleoporin Fxfg Repeats Authors: Bayliss, R. / Leung, S. / Baker, R. / Quimby, B. / Corbett, A. / Stewart, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gyb.cif.gz | 117 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gyb.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gyb ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gyb | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14512.100 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P33331 #2: Protein/peptide | Mass: 931.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: 100MM AMMONIUM ACETATE PH 6.5, 1.6M AMMONIUM SULPHATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→53 Å / Num. obs: 39224 / % possible obs: 92.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3 |
Reflection | *PLUS Lowest resolution: 53 Å / Num. measured all: 266201 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 88.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |