[English] 日本語
Yorodumi- PDB-2hnv: Crystal Structure of a Dipeptide Complex of the Q58V Mutant of Bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hnv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Dipeptide Complex of the Q58V Mutant of Bovine Neurophysin-I | ||||||
Components | Oxytocin-neurophysin 1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / protein-pepide complex / Q58V mutant / inter-domain loop / beta sheet / 3 / 10 helix | ||||||
Function / homology | Function and homology information Vasopressin-like receptors / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / G alpha (q) signalling events / secretory granule / response to estrogen / positive regulation of cold-induced thermogenesis / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Li, X. / Lee, H. / Wu, J. / Breslow, E. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand-facilitated dimerization of neurophysin: crystal structures and mutation studies of bovine neurophysin-I. Authors: Li, X. / Lee, H. / Wu, J. / Breslow, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hnv.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hnv.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/2hnv ftp://data.pdbj.org/pub/pdb/validation_reports/hn/2hnv | HTTPS FTP |
---|
-Related structure data
Related structure data | 2hnuSC 2hnwC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a dimer. There are 2.5 biological units per asymmetric unit. The complete dimers are comprised of chains A & B and chains C & D. Chain E is half of a dimer from another asymmetric unit. |
-Components
#1: Protein | Mass: 8134.256 Da / Num. of mol.: 5 / Fragment: Residues 38-118 / Mutation: Q58V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: OXT / Plasmid: pTHMa30-51 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)p Lys S / References: UniProt: P01175 #2: Chemical | ChemComp-PHE / #3: Chemical | ChemComp-TYR / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate, 22% v/v isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.541 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: VariMax-HR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→38.66 Å / Num. obs: 17407 / % possible obs: 99.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.002 / Net I/σ(I): 15.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 2HNU Resolution: 2.5→22.04 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 623573.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.583 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→22.04 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|