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Open data
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Basic information
Entry | Database: PDB / ID: 5mjc | ||||||
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Title | metNeuroglobin under oxygen at 50 bar | ||||||
![]() | Neuroglobin | ||||||
![]() | TRANSPORT PROTEIN / oxygen complex storage cavity | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prange, T. / Colloc'h, N. / Carpentier, P. / Vallone, B. | ||||||
![]() | ![]() 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 | ![]() | 50.6 KB | Display | ![]() |
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PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mjdC ![]() 6i3tC ![]() 6i40C ![]() 4o4tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16634.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 149 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-OXY / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % / 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, PH 6.5, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP |
-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: 1.55→59.66 Å / Num. obs: 20818 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.55→1.7 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4O4T Resolution: 1.62→62.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.623 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / 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: 28.663 Å2
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Refinement step | Cycle: 1 / Resolution: 1.62→62.8 Å
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Refine LS restraints |
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