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- PDB-6mv0: CO-bound Sperm Whale Myoglobin, room temperature structure solved... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mv0 | |||||||||
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Title | CO-bound Sperm Whale Myoglobin, room temperature structure solved by serial 5degree oscillation crystallography | |||||||||
![]() | Myoglobin | |||||||||
![]() | TRANSPORT PROTEIN / oxygen transporter / 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 | ![]() ![]() ![]() | |||||||||
![]() | Finke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fixed-target serial oscillation crystallography at room temperature. Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 828.2 KB | Display | ![]() |
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Full document | ![]() | 830.7 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6muhC ![]() 6muyC ![]() 6muzC ![]() 6mzzC ![]() 6n00C ![]() 6n02C ![]() 6n03C ![]() 1vxaS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17366.148 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-CMO / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.28 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 9 Details: 10 mM Tris-HCl pH 9.0 and 3.2 M ammonium sulfate and washed two to three times with the same solution (CO saturated) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018 / Details: Be compound refractive lens |
Radiation | Monochromator: W/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2155 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→40.16 Å / Num. obs: 10477 / % possible obs: 99.83 % / Redundancy: 22.6 % / Biso Wilson estimate: 42.37 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.2541 / Net I/σ(I): 10.93 |
Reflection shell | Resolution: 1.97→2.04 Å / Num. unique obs: 1006 / CC1/2: 0.181 / Rrim(I) all: 0.1648 |
Serial crystallography sample delivery | Description: fixed target Si microchips / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Si microchips / Sample holding: wells / Sample unit size: 20 µm / Support base: goniometer |
Serial crystallography data reduction | Crystal hits: 2542 / Frame hits: 63550 / Frames indexed: 20750 / Frames total: 160000 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vxa Resolution: 1.97→40.16 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 30.6325
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→40.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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