+Open data
-Basic information
Entry | Database: PDB / ID: 3vau | ||||||
---|---|---|---|---|---|---|---|
Title | Myoglobin nitrite structure: nitriheme modified | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / myoglobin / nitrite / nitriheme | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yi, J. / Richter-Addo, G.B. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2012 Title: Unveiling the three-dimensional structure of the green pigment of nitrite-cured meat Authors: Yi, J. / Richter-Addo, G.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vau.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vau.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vau_validation.pdf.gz | 785.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3vau_full_validation.pdf.gz | 788.4 KB | Display | |
Data in XML | 3vau_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 3vau_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/3vau ftp://data.pdbj.org/pub/pdb/validation_reports/va/3vau | HTTPS FTP |
-Related structure data
Related structure data | 1dwrS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: heart / References: UniProt: P68082 |
---|---|
#2: Chemical | ChemComp-NTE / [ |
#3: Chemical | ChemComp-NO2 / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.95 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: ammonium sulfate, 100mM TrisHCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 23, 2010 / Details: Osmic |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→26.34 Å / Num. all: 13478 / Num. obs: 13475 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.87 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1362 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DWR Resolution: 1.7→26.34 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.387 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.126 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.304 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→26.34 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|