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- PDB-2v1f: Crystal structure of radiation-induced myoglobin compound II - in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v1f | ||||||
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Title | Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 8.7 | ||||||
![]() | MYOGLOBIN | ||||||
![]() | OXYGEN TRANSPORT / MUSCLE PROTEIN / OXYGEN ACTIVATION / PEROXIDASE / MONOOXYGENASE / METAL-BINDING / REACTION INTERMEDIATE / HEME / FERRYL / TRANSPORT / HAEM / IRON / RADIATION | ||||||
Function / homology | ![]() nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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 | ![]() ![]() ![]() | ||||||
![]() | Hersleth, H.-P. / Gorbitz, C.H. / Andersson, K.K. | ||||||
![]() | ![]() Title: Crystallographic and Spectroscopic Studies of Peroxide-Derived Myoglobin Compound II and Occurrence of Protonated Fe(Iv)-O Authors: Hersleth, H.-P. / Uchida, T. / Rohr, A.K. / Teschner, T. / Schunemann, V. / Kitagawa, T. / Trautwein, A.X. / Gorbitz, C.H. / Andersson, K.K. #1: ![]() Title: An Iron Hydroxide Moiety in the 1.35 A Resolution Structure of Hydrogen Peroxide Derived Myoglobin Compound II at Ph 5.2. Authors: Hersleth, H. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.4 KB | Display | ![]() |
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PDB format | ![]() | 68.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v1eC ![]() 2v1gC ![]() 2v1hC ![]() 2v1iC ![]() 2v1jC ![]() 2v1kC ![]() 1gjnS S: Starting model for refinement C: citing same article ( |
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Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FE(IV)-OH / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 222 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-OH / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.39 Å3/Da / Density % sol: 32.3 % |
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Crystal grow | pH: 8.7 Details: BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M TAPS AND 5-10% OF GLYCEROL PH 8.7) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8727 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→34.3 Å / Num. obs: 38266 / % possible obs: 99.1 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.14 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GJN Resolution: 1.2→34 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.464 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.042 / 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: 13.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→34 Å
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