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Yorodumi- PDB-1xch: MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xch | ||||||
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Title | MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / MUSCLE | ||||||
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 / oxygen carrier activity / peroxidase activity / oxygen binding / 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 / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Maurus, R. / Brayer, G.D. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Structural Characterization of Heme Ligation in the His64-->Tyr Variant of Myoglobin Authors: Maurus, R. / Bogumil, R. / Luo, Y. / Tang, H.L. / Smith, M. / Mauk, A.G. / Brayer, G.D. #2: Journal: Biochemistry / Year: 1994 Title: Ftir Analysis of the Interaction of Azide with Horse Heart Myoglobin Variants Authors: Bogumil, R. / Hunter, C.L. / Maurus, R. / Tang, H.L. / Lee, H. / Lloyd, E. / Brayer, G.D. / Smith, M. / Mauk, A.G. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-Dimensional Structure of Cyanomet-Sulfmyoglobin C Authors: Evans, S.V. / Sishta, B.P. / Mauk, A.G. / Brayer, G.D. #4: Journal: J.Mol.Biol. / Year: 1990 Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin Authors: Evans, S.V. / Brayer, G.D. #5: Journal: J.Biol.Chem. / Year: 1988 Title: Horse Heart Metmyoglobin. A 2.8-A Resolution Three-Dimensional Structure Determination Authors: Evans, S.V. / Brayer, G.D. #6: 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 | 1xch.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xch.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/1xch ftp://data.pdbj.org/pub/pdb/validation_reports/xc/1xch | HTTPS FTP |
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-Related 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: 16984.459 Da / Num. of mol.: 1 / Mutation: L104N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / Production host: Escherichia coli (E. coli) / Strain (production host): LE392 / References: UniProt: P68082 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: 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: 1.88 Å3/Da / Density % sol: 34.61 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.4 Details: 20 MM TRIS/HCL, 1MM EDTA, PH 8.4, 8 MG/ML PROTEIN 69% AMMONIUM SULFATE | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 17, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. obs: 12442 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 3.91 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.5 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 18.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Software | *PLUS Name: GPRLSA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |