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Yorodumi- PDB-5zeo: X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zeo | ||||||
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Title | X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant with an intramolecular disulfide bond | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / myoglobin / sperm whale | ||||||
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: 1.77 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2018 Title: Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin Authors: Yin, L.L. / Yuan, H. / Du, K.J. / He, B. / Gao, S.Q. / Wen, G.B. / 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 | 5zeo.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zeo.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zeo_validation.pdf.gz | 841.8 KB | Display | wwPDB validaton report |
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Full document | 5zeo_full_validation.pdf.gz | 846.6 KB | Display | |
Data in XML | 5zeo_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5zeo_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5zeo ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5zeo | HTTPS FTP |
-Related structure data
Related structure data | 5hlxS 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: 17182.879 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: V21C, P46S, V66C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (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 / |
-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: 42.96 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→40.63 Å / Num. obs: 15020 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 23.05 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.33 / Num. unique obs: 725 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HLX Resolution: 1.77→40.63 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.77→40.63 Å
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