+Open data
-Basic information
Entry | Database: PDB / ID: 7v5r | ||||||||||||
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Title | The dimeric structure of G80A/H81A/L137D myoglobin | ||||||||||||
Components | Myoglobin | ||||||||||||
Keywords | OXYGEN BINDING / OXYGEN STORAGE | ||||||||||||
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 / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Equus caballus (horse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||||||||
Authors | Xie, C. / Komori, H. / Hirota, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Rsc Adv / Year: 2021 Title: Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region. Authors: Xie, C. / Shimoyama, H. / Yamanaka, M. / Nagao, S. / Komori, H. / Shibata, N. / Higuchi, Y. / Shigeta, Y. / Hirota, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v5r.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v5r.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 7v5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/7v5r ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v5r | HTTPS FTP |
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-Related structure data
Related structure data | 7v5pC 7v5qC 3vm9S S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153
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-Components
#1: Protein | Mass: 16932.400 Da / Num. of mol.: 2 / Mutation: G80A, H81A, L137D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 10 % (w/v) PEG 6000, and 5 % (w/v) PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→46.33 Å / Num. obs: 59149 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.018 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.39→1.41 Å / Num. unique obs: 2987 / CC1/2: 0.856 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VM9 Resolution: 1.39→46.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.68 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.262 Å2
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Refinement step | Cycle: 1 / Resolution: 1.39→46.37 Å
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Refine LS restraints |
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