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- PDB-5e7w: X-ray Structure of Human Recombinant 2Zn insulin at 0.92 Angstrom -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e7w | ||||||
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Title | X-ray Structure of Human Recombinant 2Zn insulin at 0.92 Angstrom | ||||||
![]() | (Insulin![]() | ||||||
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Function / homology | ![]() negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / Insulin processing / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lisgarten, D.R. / Naylor, C.E. / Palmer, R.A. / Lobley, C.M.C. | ||||||
![]() | ![]() Title: Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K. Authors: Lisgarten, D.R. / Palmer, R.A. / Lobley, C.M.C. / Naylor, C.E. / Chowdhry, B.Z. / Al-Kurdi, Z.I. / Badwan, A.A. / Howlin, B.J. / Gibbons, N.C.J. / Saldanha, J.W. / Lisgarten, J.N. / Basak, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.8 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3w7yS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | ![]() Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Human Insulin A and C Chain Insulin was purchased from Insugen Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | ![]() Mass: 3433.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Human Insulin B and D chain Insulin was purchased from Insugen Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 224 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-ACT / | ![]() #5: Chemical | ChemComp-POL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35 % / Description: needle |
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Crystal grow![]() | Temperature: 293 K / Method: batch mode / pH: 6.3 Details: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was ...Details: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was added to dissolve the protein; on addition of 0.15 mL of 0.15 M zinc acetate the solution became cloudy due to precipitation of the protein; 0.3 mL of acetone and then 0.5 mL of trisodium citrate together with 0.8 mL of water were added and the solution went clear; the pH was checked and increased with NaOH to a pH between 8 and 9 for different batches, thus ensuring complete dissolution. It was then adjusted to the required value of pH 6.3. If any slight turbidity occurred, it was removed by warming the solution. The solution was then filtered using a Millipore membrane/acetate cellulose acetate filter. This removes any nuclei which will encourage precipitation or formation of masses of small crystals. The solution was then warmed to 50 deg C by surrounding the test tube with preheated water in a Dewar. This allowed the solution to cool slowly to room temperature. The test tube was lightly sealed with cling film; crystals formed within a few days and were of suitable size for X-ray diffraction within two weeks; the test tube containing crystals was kept at 4 degC prior to data collection. The crystal used for data collection was about 0.2 mm3. PH range: 6.2 - 6.4 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2012 Details: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle ...Details: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle and 180 deg of data were collected with 0.1 deg oscillation and 0.1s exposure. The resolution of useful diffraction data achieved and used for structure analysis was 0.92 Angstrom. |
Radiation | Monochromator: Beamline fixed at 16000keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.92→40.91 Å / Num. obs: 58647 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 0.92→0.94 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3W7Y Resolution: 0.9519→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso mean: 18.45 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9519→10 Å
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