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- PDB-2vlx: Crystal structure of peroxymyoglobin generated by cryoradiolytic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vlx | ||||||
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Title | Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III | ||||||
![]() | MYOGLOBIN | ||||||
![]() | OXYGEN TRANSPORT / HAEM / IRON / HEME / FERRYL / TRANSPORT / PEROXIDASE / OXYGEN ACTIVATION / RADIOLYTIC- REDUCTION / REACTION INTERMEDIATE / MONOOXYGENASE / METAL-BINDING / MUSCLE PROTEIN / X-RAY-INDUCED-PHOTOREDUCTION | ||||||
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: The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection. Authors: Hersleth, H.-P. / Hsiao, Y.-W. / Ryde, U. / 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 | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 830.2 KB | Display | ![]() |
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Full document | ![]() | 830.8 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vlyC ![]() 2vlzC ![]() 2vm0C ![]() 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 / Fragment: RESIDUES 2-154 / Source method: isolated from a natural source / Details: FE(III)OO2- / FE(II)OO- / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 186 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-PER / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.47 Å3/Da / Density % sol: 15.6 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 6.8) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8727 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→33 Å / Num. obs: 29779 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GJN Resolution: 1.3→26.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.691 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.054 / 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: 17.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.6 Å
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Refine LS restraints |
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