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- PDB-5zeo: X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant wi... -
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Open data
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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 | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN TRANSPORT / myoglobin / sperm whale | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yuan, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.4 KB | Display | ![]() |
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PDB format | ![]() | 33.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.8 KB | Display | ![]() |
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Full document | ![]() | 846.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hlxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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