+
Open data
-
Basic information
Entry | Database: PDB / ID: 1n9f | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of earth-grown oxidized Myoglobin mutant YQR (ISS6A) | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / globin fold / 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. / Sciara, G. / Federici, L. / Vallone, B. / Brunori, M. | ||||||
![]() | ![]() 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 | ![]() | 47.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 32.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 831.9 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n9hC ![]() 1n9iC ![]() 1n9xC ![]() 1nazC ![]() 1f65S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | the biological assembly 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 | ChemComp-SO4 / |
#4: Chemical | ChemComp-HEM / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.87 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Ammonium sulfate, tris, EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
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 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 21977 / Num. obs: 21977 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 18.51 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.8→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 10.2 / % possible all: 86.7 |
Reflection | *PLUS Lowest resolution: 15 Å |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.83 Å / % possible obs: 86.7 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1f65 Resolution: 1.8→15 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 21.96 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|