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Open data
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Basic information
Entry | Database: PDB / ID: 7spe | ||||||
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Title | Crystal structure of sperm whale myoglobin variant sMb5(O2beY) | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE / HEME / METALLOPROTEIN / THIOETHER / MYOGLOBIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Bacik, J.P. / Fasan, R. / Ando, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Authors: Iannuzzelli, J.A. / Bacik, J.P. / Moore, E.J. / Shen, Z. / Irving, E.M. / Vargas, D.A. / Khare, S.D. / Ando, N. / Fasan, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.1 KB | Display | ![]() |
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PDB format | ![]() | 33.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 822.6 KB | Display | ![]() |
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Full document | ![]() | 824.2 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7spfC ![]() 7spgC ![]() 7sphC ![]() 6m8fS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17420.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 160 nl of protein (1 mM) in 20 mM Tris pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution, 3.0 M ammonium sulfate, 10% w/v glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Oct 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 14910 / % possible obs: 89.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.75 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.074 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.578 / Num. unique obs: 430 / CC1/2: 0.634 / Rpim(I) all: 0.542 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M8F Resolution: 1.7→27.192 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.74 Å2 / Biso mean: 16.3581 Å2 / Biso min: 5.88 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→27.192 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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