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Open data
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Basic information
Entry | Database: PDB / ID: 6r1q | ||||||
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Title | murine Neuroglobin under 2 kBar of argon | ||||||
![]() | Neuroglobin | ||||||
![]() | OXYGEN STORAGE / neuroglobin / argon / high pressure | ||||||
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. / Vallone, B. | ||||||
![]() | ![]() Title: Argon-labelling protein crystals by high pressure cooling at 2000 Bar Authors: Prange, T. / Colloc'h, N. / Carpentier, P. / van Linden, P. #1: ![]() Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.1 KB | Display | ![]() |
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Full document | ![]() | 840.8 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4o4tS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16634.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS 55 and CYS 120 mutated in SER residues / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 119 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||||
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#3: Chemical | ChemComp-HEM / | ||||
#4: Chemical | ChemComp-AR / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: Deep red cubes |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 1.6M AMMONIUM SULPHATE, 0.1M MES, PH 6.5, 10 % DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2018 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.771 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.35 Å / Num. obs: 15605 / % possible obs: 98.8 % / Redundancy: 16.3 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.019 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2089 / Rpim(I) all: 0.206 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4o4T Resolution: 1.95→44.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.353 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.178 / 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: 38.248 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→44.01 Å
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Refine LS restraints |
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