[English] 日本語
Yorodumi- PDB-1t1v: Crystal Structure of the Glutaredoxin-like Protein SH3BGRL3 at 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t1v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Glutaredoxin-like Protein SH3BGRL3 at 1.6 A resolution | ||||||
Components | SH3 domain-binding glutamic acid-rich protein-like 3 | ||||||
Keywords | SIGNALING PROTEIN / GLUTAREDOXIN / THIOREDOXIN FOLD / PROTEIN 3D-STRUCTURE / X-RAY CRYSTALLOGRAPHY | ||||||
Function / homology | Function and homology information cytoskeleton organization / ruffle membrane / nuclear body / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Nardini, M. / Mazzocco, M. / Massaro, M. / Maffei, M. / Vergano, A. / Donadini, A. / Scartezzini, M. / Bolognesi, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Crystal structure of the glutaredoxin-like protein SH3BGRL3 at 1.6 A resolution Authors: Nardini, M. / Mazzocco, M. / Massaro, M. / Maffei, M. / Vergano, A. / Donadini, A. / Scartezzini, M. / Bolognesi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t1v.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t1v.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 1t1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/1t1v ftp://data.pdbj.org/pub/pdb/validation_reports/t1/1t1v | HTTPS FTP |
---|
-Related structure data
Related structure data | 1j0fS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10487.724 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q91VW3 #2: Chemical | ChemComp-GOL / | #3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 36.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Ammonium sulfate, Na-acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→34.5 Å / Num. all: 21080 / Num. obs: 18915 / % possible obs: 99.4 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J0F Resolution: 1.6→34.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.205 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→34.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.645 Å / Total num. of bins used: 20 /
|