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- PDB-7spg: Crystal structure of sperm whale myoglobin variant sMb13(pCaaF) i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7spg | ||||||
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Title | Crystal structure of sperm whale myoglobin variant sMb13(pCaaF) in space group P212121 | ||||||
![]() | 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 | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.6 KB | Display | ![]() |
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Full document | ![]() | 827.2 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7speC ![]() 7spfSC ![]() 7sphC 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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Unit cell |
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Components
#1: Protein | Mass: 17464.395 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 | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 160 nl of protein (2.15 mM) in 20 mM Tris pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution, 1.6 M ammonium sulfate, 0.5 M lithium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→35.73 Å / Num. obs: 39628 / % possible obs: 99.5 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 1.278 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1961 / CC1/2: 0.715 / Rpim(I) all: 0.427 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7SPF Resolution: 1.3→35.727 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.24 / 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: 86.62 Å2 / Biso mean: 28.8043 Å2 / Biso min: 15.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→35.727 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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