+Open data
-Basic information
Entry | Database: PDB / ID: 2vly | ||||||
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Title | Crystal structure of myoglobin compound III (radiation-induced) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX / HAEM / IRON / HEME / FERRYL / TRANSPORT / PEROXIDASE / OXYGEN ACTIVATION / RADIOLYTIC- REDUCTION / REACTION INTERMEDIATE / MONOOXYGENASE / METAL-BINDING / MUSCLE PROTEIN / X-RAY-INDUCED-PHOTOREDUCTION | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hersleth, H.-P. / Gorbitz, C.H. / Andersson, K.K. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection. Authors: Hersleth, H.-P. / Hsiao, Y. / Ryde, U. / Gorbitz, C.H. / Andersson, K.K. #1: Journal: J.Biol.Inorg.Chem. / Year: 2002 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.-P. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vly.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vly.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vly ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vly | HTTPS FTP |
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-Related structure data
Related structure data | 2vlxC 2vlzC 2vm0C 1gjnS 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 / Fragment: RESIDUES 2-154 / Source method: isolated from a natural source / Details: FE(III)OO- / FE(II)OO / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P68082 |
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-Non-polymers , 6 types, 169 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-OXY / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 1.5 Å3/Da / Density % sol: 33.09 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: CRYSTALLIZATION CONDITIONS: 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→21.97 Å / Num. obs: 16256 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.74 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.74 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.14 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GJN Resolution: 1.6→21.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.394 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE IS FIRST OF THREE DATASETS COLLECTED ON THE SAME CRYSTAL AS 2VLZ AND 2VM0.
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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: 16.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→21.94 Å
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Refine LS restraints |
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