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Yorodumi- PDB-3m3a: The roles of glutamates and metal ions in a rationally designed n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m3a | ||||||
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Title | The roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin: Cu(II)-I107E FeBMb (Cu(II) binding to FeB site) | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Alpha Helix / Heme protein / Metal-binding / NO reductase | ||||||
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 / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.37 Å | ||||||
Authors | Lin, Y.-W. / Yeung, N. / Gao, Y.-G. / Miner, K.D. / Tian, S. / Robinson, H. / Lu, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin. Authors: Lin, Y.W. / Yeung, N. / Gao, Y.G. / Miner, K.D. / Tian, S. / Robinson, H. / Lu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m3a.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m3a.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 3m3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m3a_validation.pdf.gz | 785.4 KB | Display | wwPDB validaton report |
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Full document | 3m3a_full_validation.pdf.gz | 793.4 KB | Display | |
Data in XML | 3m3a_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3m3a_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3a ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | P41 |
-Components
#1: Protein | Mass: 17296.854 Da / Num. of mol.: 1 / Mutation: L29H, F43H, V68E, I107E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.33 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.089 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.089 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→32.33 Å / Num. obs: 29149 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: NONE Resolution: 1.37→10 Å / Num. parameters: 5735 / Num. restraintsaints: 5217 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1430 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→10 Å
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Refine LS restraints |
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