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Yorodumi- PDB-7a44: CO-bound sperm whale myoglobin measured by serial synchrotron cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a44 | ||||||
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Title | CO-bound sperm whale myoglobin measured by serial synchrotron crystallography | ||||||
Components | Myoglobin | ||||||
Keywords | METAL BINDING PROTEIN / co-bound / myoglobin / serial crystallography | ||||||
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: 1.75 Å | ||||||
Authors | Mehrabi, P. / Schulz, E.C. / Buecker, R. | ||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. Authors: Mehrabi, P. / Bucker, R. / Bourenkov, G. / Ginn, H.M. / von Stetten, D. / Muller-Werkmeister, H.M. / Kuo, A. / Morizumi, T. / Eger, B.T. / Ou, W.L. / Oghbaey, S. / Sarracini, A. / Besaw, J.E. ...Authors: Mehrabi, P. / Bucker, R. / Bourenkov, G. / Ginn, H.M. / von Stetten, D. / Muller-Werkmeister, H.M. / Kuo, A. / Morizumi, T. / Eger, B.T. / Ou, W.L. / Oghbaey, S. / Sarracini, A. / Besaw, J.E. / Pare-Labrosse, O. / Meier, S. / Schikora, H. / Tellkamp, F. / Marx, A. / Sherrell, D.A. / Axford, D. / Owen, R.L. / Ernst, O.P. / Pai, E.F. / Schulz, E.C. / Miller, R.J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a44.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a44.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 7a44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a44 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a44 | HTTPS FTP |
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-Related structure data
Related structure data | 7a42C 7a43C 7a45C 5jomS S: Starting model for refinement C: citing same article (ref.) |
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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: 17365.164 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-SO4 / |
#4: Chemical | ChemComp-CMO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: 10 mM Tris-HCl, pH 9.0, 2.2-2.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→31.47 Å / Num. obs: 15863 / % possible obs: 99.53 % / Redundancy: 114.79 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.9733 / Net I/σ(I): 5.54 |
Reflection shell | Resolution: 1.75→1.813 Å / Num. unique obs: 1492 / CC1/2: 0.5003 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JOM Resolution: 1.75→31.47 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.1812 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→31.47 Å
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Refine LS restraints |
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LS refinement shell |
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