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Yorodumi- PDB-7vdn: High resolution crystal structure of Sperm Whale Myoglobin in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vdn | ||||||
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Title | High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / myoglobin / blood / Heme binding / Metal ion binding | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.93 Å | ||||||
Authors | Shibayama, N. / Sato-Tomita, A. / Ishimoto, N. / Park, S.Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: X-ray fluorescence holography of biological metal sites: Application to myoglobin. Authors: Sato-Tomita, A. / Ang, A.K.R. / Kimura, K. / Marumi, R. / Happo, N. / Matsushita, T. / Park, S.Y. / Shibayama, N. / Sasaki, Y.C. / Hayashi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vdn.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vdn.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vdn ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vdn | HTTPS FTP |
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-Related structure data
Related structure data | 1vxcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17049.771 Da / Num. of mol.: 1 / Fragment: UNP residues 2-152 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #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: 1.9 Å3/Da / Density % sol: 35.39 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 2.8 M ammonium sulfate, 50 mM K2HPO4, 50 mM NaH2PO4, 10% glycerol, 2 mg/ml sodium dithionite |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 0.93→20.02 Å / Num. obs: 86393 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 8.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Χ2: 0.87 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 0.93→0.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4341 / CC1/2: 0.069 / Χ2: 0.98 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VXC Resolution: 0.93→20.02 Å / SU ML: 0.1836 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4175 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: 15.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.93→20.02 Å
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Refine LS restraints |
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LS refinement shell |
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