+Open data
-Basic information
Entry | Database: PDB / ID: 6krc | ||||||
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Title | An X-ray structure of ferric F43Y/F46S sperm whale myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / myoglobin | ||||||
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 / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter macrocephalus (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Yuan, H. / Lin, Y.W. | ||||||
Citation | Journal: Acs Catalysis / Year: 2020 Title: A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases. Authors: Zhang, P. / Yuan, H. / Xu, J. / Wang, X.J. / Gao, S.Q. / Tan, X. / Lin, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6krc.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6krc.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 6krc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6krc ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6krc | HTTPS FTP |
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-Related structure data
Related structure data | 6krfC 5xkvS 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: 17190.855 Da / Num. of mol.: 1 / Mutation: F43Y, F46S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG8000, 0.1 M NaAc, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→50 Å / Num. obs: 31430 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.39→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2147 / Rpim(I) all: 0.482 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XKV Resolution: 1.39→30.72 Å / SU ML: 0.1146 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.9515
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→30.72 Å
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Refine LS restraints |
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LS refinement shell |
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