+Open data
-Basic information
Entry | Database: PDB / ID: 6q8q | ||||||
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Title | Bovine Insulin under 2 kbar of argon | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE / insulin / argon / high pressure | ||||||
Function / homology | Function and homology information estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / positive regulation of insulin secretion / hormone activity / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Prange, T. / Carpentier, P. | ||||||
Citation | Journal: To be published Title: Argon-labelling protein crystals by high pressure cooling at 2 kbar Authors: Prange, T. / Carpentier, P. #1: Journal: Journal of Applied Crystallography / Year: 2016 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. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q8q.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8q.ent.gz | 14.3 KB | Display | PDB format |
PDBx/mmJSON format | 6q8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q8q_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 6q8q_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 6q8q_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 6q8q_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8q ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8q | HTTPS FTP |
-Related structure data
Related structure data | 3bn3S 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
#1: Protein/peptide | Mass: 2369.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Insulin chain A / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 |
#3: Chemical | ChemComp-AR / |
#4: 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: 3.55 Å3/Da / Density % sol: 65.5 % / Description: COLORLESS PRISMATIC |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PROTEIN DROP: 10 MG/ML. RESERVOIR: 1.2 M TMAO + 0.1 M SODIUM MALATE, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.9997 Å |
Detector | Type: DECTRIS PILATUS3 S 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: 1.9997 Å / Relative weight: 1 |
Reflection | Resolution: 2→39 Å / Num. obs: 5259 / % possible obs: 97.8 % / Redundancy: 30.4 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.016 / Rrim(I) all: 0.081 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 673 / Rpim(I) all: 0.087 / Rrim(I) all: 0.218 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BN3 Resolution: 2→38.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.947 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.123
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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: 29.976 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.81 Å
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