+Open data
-Basic information
Entry | Database: PDB / ID: 4fwz | ||||||
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Title | Aquoferric CuB myoglobin (L29H F43H sperm whale myoglobin) | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / Globin / Oxidase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gao, Y.-G. / 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 | 4fwz.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwz.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fwz_validation.pdf.gz | 783.8 KB | Display | wwPDB validaton report |
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Full document | 4fwz_full_validation.pdf.gz | 789 KB | Display | |
Data in XML | 4fwz_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 4fwz_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwz ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwz | HTTPS FTP |
-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: 17250.914 Da / Num. of mol.: 1 / Mutation: L29H, 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: 2.13 Å3/Da / Density % sol: 42.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: CuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% ...Details: CuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% polyethylene glycol 4000) 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: X12B / Wavelength: 0.894 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.894 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 12087 / Num. obs: 12087 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 9.8 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: SHELX DEFAULT
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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