+Open data
-Basic information
Entry | Database: PDB / ID: 6ltl | ||||||||||||
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Title | The dimeric structure of G80A myoglobin | ||||||||||||
Components | Myoglobin | ||||||||||||
Keywords | OXYGEN BINDING / OXYGEN STORAGE | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Equus caballus (horse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||||||||
Authors | Nagao, S. / Suda, A. / Kobayashi, H. / Shibata, N. / Higuchi, Y. / Hirota, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Chem Asian J / Year: 2020 Title: Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin. Authors: Nagao, S. / Suda, A. / Kobayashi, H. / Shibata, N. / Higuchi, 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 | 6ltl.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ltl.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ltl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ltl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ltl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ltl_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6ltl_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltl ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltl | HTTPS FTP |
-Related structure data
Related structure data | 6ls8C 6ltmC 3vm9S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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: _ / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153
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-Components
#1: Protein | Mass: 16997.539 Da / Num. of mol.: 2 / Mutation: G80A 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: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Tris-HCl buffer, 0.1M sodium acetate, 10% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 85063 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.25→1.28 Å / Rmerge(I) obs: 0.918 / Num. unique obs: 4107 / CC1/2: 0.849 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VM9 Resolution: 1.25→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.91 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.073 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→50 Å
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Refine LS restraints |
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