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Yorodumi- PDB-4fwx: Aquoferric F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwx | ||||||
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Title | Aquoferric F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin) | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / Globin / Oxidase | ||||||
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: 1.9 Å | ||||||
Authors | Gao, Y.-G. / Stoner-Ma, D. / Robinson, H. / Petrik, I.D. / Miner, K.D. / Lu, Y. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 Title: A Designed Functional Metalloenzyme that Reduces O(2) to H(2) O with Over One Thousand Turnovers. Authors: Miner, K.D. / Mukherjee, A. / Gao, Y.G. / Null, E.L. / Petrik, I.D. / Zhao, X. / Yeung, N. / 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 | 4fwx.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwx.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fwx_validation.pdf.gz | 805.3 KB | Display | wwPDB validaton report |
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Full document | 4fwx_full_validation.pdf.gz | 808.7 KB | Display | |
Data in XML | 4fwx_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4fwx_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwx ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwx | HTTPS FTP |
-Related structure data
Related structure data | 4fwyC 4fwzSC 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
#1: Protein | Mass: 17266.914 Da / Num. of mol.: 1 / Mutation: L29H, F33Y, F43H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3*) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: F33Y-CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol ...Details: F33Y-CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol 8000) using the hanging drop method with 300 uL well buffer in the well of the crystallization tray, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 12106 / Num. obs: 12106 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.118 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FWZ Resolution: 1.9→40.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.65 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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