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Yorodumi- PDB-2evk: The Structures of Thiolate- and Carboxylate-Ligated Ferric H93G M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2evk | ||||||
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Title | The Structures of Thiolate- and Carboxylate-Ligated Ferric H93G Myoglobin: Models for Cytochrome P450 and for Oxyanion-Bound Heme Proteins | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / H93G / HEME / Acetate / BME / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / 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 | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Qin, J. / Perera, R. / Lovelace, L.L. / Dawson, J.H. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structures of thiolate- and carboxylate-ligated ferric H93G myoglobin: models for cytochrome P450 and for oxyanion-bound heme proteins. Authors: Qin, J. / Perera, R. / Lovelace, L.L. / Dawson, J.H. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2evk.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2evk.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 2evk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2evk_validation.pdf.gz | 813.4 KB | Display | wwPDB validaton report |
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Full document | 2evk_full_validation.pdf.gz | 817.9 KB | Display | |
Data in XML | 2evk_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 2evk_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/2evk ftp://data.pdbj.org/pub/pdb/validation_reports/ev/2evk | HTTPS FTP |
-Related structure data
Related structure data | 2evpC 1dtmS S: Starting model for refinement C: citing same article (ref.) |
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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: 17153.857 Da / Num. of mol.: 1 / Mutation: H93G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pMb413b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lambda DE3) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ACY / |
#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: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 37% PEG 8K, 300mM sodium Acetate, 0.1M PIPES, 0.1% dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97929 Å |
Detector | Date: Jun 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 26514 |
Reflection shell | Resolution: 1.4→1.45 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DTM Resolution: 1.4→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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