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Open data
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Basic information
Entry | Database: PDB / ID: 3hc9 | ||||||
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Title | Ferric Horse Heart Myoglobin; H64V mutant | ||||||
![]() | Myoglobin![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yi, J. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.3 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.7 KB | Display | ![]() |
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Full document | ![]() | 774.1 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16944.498 Da / Num. of mol.: 1 / Mutation: H64V Source method: isolated from a genetically manipulated source Details: Heart / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / ![]() |
#3: Chemical | ChemComp-PO4 / ![]() |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.74 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: ammonium phosphate, EDTA, horse heart myoglobin H64V mutant, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 2, 2009 / Details: Osmic |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→20.8 Å / Num. obs: 15752 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.42 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.44 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1431 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Model was generated by Balbes Resolution: 2→20.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.52 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.151 / ESU R Free: 0.15 / 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: 27.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.226 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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