+Open data
-Basic information
Entry | Database: PDB / ID: 6ra6 | ||||||
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Title | Ferric murine neuroglobin Gly-loop44-47/F106A mutant | ||||||
Components | Neuroglobin,Murine neuroglobin mutant,Neuroglobin | ||||||
Keywords | OXYGEN BINDING / heme protein / globin / gas binding | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Exertier, C. / Freda, I. / Montemiglio, L.C. / Savino, C. / Vallone, B. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Febs J. / Year: 2020 Title: Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy. Authors: Milazzo, L. / Exertier, C. / Becucci, M. / Freda, I. / Montemiglio, L.C. / Savino, C. / Vallone, B. / Smulevich, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ra6.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ra6.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 6ra6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6ra6 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ra6 | HTTPS FTP |
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-Related structure data
Related structure data | 6h6iS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16464.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct. ...Details: For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ER97 |
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-Non-polymers , 6 types, 73 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-TRS / | ||||
#5: Chemical | #6: Chemical | #7: 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: 3.91 Å3/Da / Density % sol: 68.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.8 M ammonium sulfate, 0.1 M Tris pH 8.5, 1% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.32 Å / Num. obs: 10869 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.12 / Net I/σ(I): 17.35 |
Reflection shell | Resolution: 2.3→2.49 Å / Redundancy: 11.31 % / Mean I/σ(I) obs: 2.34 / Num. unique obs: 3693 / CC1/2: 0.81 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H6I Resolution: 2.3→37.32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.727 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.185 / 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: 49.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37.32 Å
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Refine LS restraints |
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