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Open data
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Basic information
Entry | Database: PDB / ID: 5b84 | ||||||
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Title | X-ray crystal structure of met I107Y sperm whale myoglobin | ||||||
![]() | Myoglobin![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yuan, H. | ||||||
![]() | ![]() Title: Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin Authors: Liao, F. / Yuan, H. / Du, K.J. / You, Y. / Gao, S.Q. / Wen, G.B. / Lin, Y.W. / Tan, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b85C ![]() 4qauS C: citing same article ( 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: 17284.969 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: I107Y 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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%(w/v) Polyethylene glycol 8,000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→50 Å / Num. obs: 19658 / % possible obs: 96.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4QAU Resolution: 1.61→35.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.713 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.091 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→35.57 Å
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Refine LS restraints |
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