+Open data
-Basic information
Entry | Database: PDB / ID: 3v2v | ||||||
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Title | Nitrite Bound Chlorin Substituted Myoglobin- Method 1 | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / nitrite / chlorin / myoglobin / chlorin reconstituted myoglobin | ||||||
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: 1.65 Å | ||||||
Authors | Yi, J. / Thomas, L.M. / Ricther-Addo, G.B. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 Title: Distal pocket control of nitrite binding in myoglobin Authors: Yi, J. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v2v.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v2v.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 3v2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v2v_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3v2v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3v2v_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3v2v_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/3v2v ftp://data.pdbj.org/pub/pdb/validation_reports/v2/3v2v | HTTPS FTP |
-Related structure data
Related structure data | 3v2zC 3ba2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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 |
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-Non-polymers , 5 types, 157 molecules
#2: Chemical | ChemComp-HKL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.19 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 21, 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: 1.65→26.45 Å / Num. obs: 15443 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.13 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1503 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BA2 Resolution: 1.65→26.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.298 / SU ML: 0.078 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.128 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.747 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→26.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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