+Open data
-Basic information
Entry | Database: PDB / ID: 1gjn | ||||||
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Title | Hydrogen Peroxide Derived Myoglobin Compound II at pH 5.2 | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / REACTION INTERMEDIATE / HAEM / HEME / OXYGEN ACTIVATION / PEROXIDASE / MONOOXYGENASE / FERRYL / HYDROXY RADICAL | ||||||
Function / homology | Function and homology information 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 / 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: 1.35 Å | ||||||
Authors | Hersleth, H.-P. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K. | ||||||
Citation | 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. #1: Journal: Biochim.Biophys.Acta / Year: 1997 Title: A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket Authors: Maurus, R. / Overall, C.M. / Bogumil, R. / Luo, Y. / Mauk, A.G. / Smith, M. / Brayer, G.D. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gjn.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gjn.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/1gjn ftp://data.pdbj.org/pub/pdb/validation_reports/gj/1gjn | HTTPS FTP |
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-Related structure data
Related structure data | 1wlaS 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
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: A FE(III)-BONDED HYDROXYL RADICAL / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P02188, UniProt: P68082*PLUS | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-OH / | ||
#4: Chemical | #5: 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: 1.8 Å3/Da / Density % sol: 31.76 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.2 Details: 6-10 MG/ML PROTEIN 3.0 M AMMONIUM SULPHATE, 10.8% GLYCEROL PH 5.2, RT. | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→21 Å / Num. obs: 26717 / % possible obs: 98.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.7 / % possible all: 85.4 |
Reflection | *PLUS Lowest resolution: 21 Å / Num. measured all: 296944 |
Reflection shell | *PLUS % possible obs: 85.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WLA Resolution: 1.35→20.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2057058.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.5094 Å2 / ksol: 0.438879 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→20.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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