[English] 日本語
![](img/lk-miru.gif)
- PDB-1naz: structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1naz | ||||||
---|---|---|---|---|---|---|---|
Title | structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A) | ||||||
![]() | Myoglobin | ||||||
![]() | oxygen storage/transport / globin fold / nearly-atomic resolution / microgravity / oxygen storage-transport COMPLEX | ||||||
Function / homology | ![]() nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miele, A.E. / Federici, L. / Sciara, G. / Draghi, F. / Brunori, M. / Vallone, B. | ||||||
![]() | ![]() Title: Analysis of the effect of microgravity on protein crystal quality: the case of a myoglobin triple mutant. Authors: Miele, A.E. / Federici, L. / Sciara, G. / Draghi, F. / Brunori, M. / Vallone, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 806.9 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n9fC ![]() 1n9hC ![]() 1n9iC ![]() 1n9xC ![]() 1f65S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | the protein is a monomer |
-
Components
#1: Protein | Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-OH / | ||||
#3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: ammonium sulfate, tris, EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→20 Å / Num. obs: 99221 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.31 % / Biso Wilson estimate: 8.874 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.04→1.07 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 18.5 / % possible all: 100 |
Reflection | *PLUS Num. obs: 97313 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 100 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb code 1f65 Resolution: 1.04→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 9.54 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.132 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|