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Yorodumi- PDB-6mv0: CO-bound Sperm Whale Myoglobin, room temperature structure solved... -
+Open data
-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 | |||||||||
Components | Myoglobin | |||||||||
Keywords | TRANSPORT PROTEIN / oxygen transporter / myoglobin | |||||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Physeter catodon (sperm whale) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Finke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: IUCrJ / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mv0.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mv0.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/6mv0 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mv0 | HTTPS FTP |
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-Related structure data
Related structure data | 6muhC 6muyC 6muzC 6mzzC 6n00C 6n02C 6n03C 1vxaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.2155 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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