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Open data
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Basic information
Entry | Database: PDB / ID: 5mjd | ||||||
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Title | metNgb under oxygen at 80 bar | ||||||
![]() | Neuroglobin | ||||||
![]() | TRANSPORT PROTEIN / oxygen complex storage cavity | ||||||
Function / homology | ![]() Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prange, T. / Colloc'h, N. / Carpentier, P. | ||||||
![]() | ![]() Title: Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. Authors: Ardiccioni, C. / Arcovito, A. / Della Longa, S. / van der Linden, P. / Bourgeois, D. / Weik, M. / Montemiglio, L.C. / Savino, C. / Avella, G. / Exertier, C. / Carpentier, P. / Prange, T. / ...Authors: Ardiccioni, C. / Arcovito, A. / Della Longa, S. / van der Linden, P. / Bourgeois, D. / Weik, M. / Montemiglio, L.C. / Savino, C. / Avella, G. / Exertier, C. / Carpentier, P. / Prange, T. / Brunori, M. / Colloc'h, N. / Vallone, B. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005 Title: Neuroglobin, nitric oxide, and oxygen: functional pathways and conformational changes. Authors: Brunori, M. / Giuffre, A. / Nienhaus, K. / Nienhaus, G.U. / Scandurra, F.M. / Vallone, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 873.7 KB | Display | ![]() |
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Full document | ![]() | 876.9 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mjcC ![]() 6i3tC ![]() 6i40C ![]() 1oj6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16634.871 Da / Num. of mol.: 1 / Mutation: S-C Source method: isolated from a genetically manipulated source Details: contains in the storage site a dioxygen molecule / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-OXY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % / Description: DEEP RED CUBES |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M AMMONIUM SULPHATE, 0.1M MES,PH6.5, 10%(V/V) DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2016 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8859 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.49 Å / Num. all: 102328 / Num. obs: 17697 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 14539 / Num. unique all: 2592 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OJ6 Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.172 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.873 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→20 Å
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Refine LS restraints |
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