+Open data
-Basic information
Entry | Database: PDB / ID: 3heo | ||||||
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Title | Ferric Horse Heart Myoglobin; H64V/V67R mutant, Nitrite Modified | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / ferric myolobin / horse heart / H64V/V67R / nitrite adduct / Heme / Iron / Metal-binding / Muscle protein / Transport | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yi, J. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: The distal pocket histidine residue in horse heart myoglobin directs the o-binding mode of nitrite to the heme iron. Authors: Yi, J. / Heinecke, J. / Tan, H. / Ford, P.C. / 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 | 3heo.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3heo.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 3heo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3heo ftp://data.pdbj.org/pub/pdb/validation_reports/he/3heo | HTTPS FTP |
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-Related structure data
Related structure data | 3hc9C 3henSC 3hepC 3hdw S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17002.562 Da / Num. of mol.: 1 / Mutation: H64V, V67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Plasmid: pGYM / Production host: Escherichia coli (E. coli) / References: UniProt: P68082 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #4: 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: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: ammonium phosphate, EDTA, crystal soaking with sodium nitrite, pH 6.8, 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: Mar 5, 2009 / Details: Osmic mirrors |
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: 2→19.83 Å / Num. obs: 13595 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.23 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.17 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2016 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry: 3HEN Resolution: 2→19.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.159 / SU ML: 0.117 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.179 / ESU R Free: 0.174 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.937 Å2
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Refine analyze | Luzzati coordinate error obs: 24.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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