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Open data
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Basic information
Entry | Database: PDB / ID: 5urt | ||||||
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Title | Insulin with proline analog DhP at position B28 in the T2 state | ||||||
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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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insulin with proline analog DhP at position B28 in the T2 state Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.7 KB | Display | ![]() |
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PDB format | ![]() | 25.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3t2aS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3431.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.86 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75 / Details: 200mM Sodium Citrate, 100mM Hepes pH 7.75 / Temp details: Room temp |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016 | |||||||||||||||||||||||||||
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.17→55.12 Å / Num. obs: 26449 / % possible obs: 99.7 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.021 / Rrim(I) all: 0.091 / Net I/σ(I): 18.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3T2A Resolution: 1.18→55.12 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.778 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 101.15 Å2 / Biso mean: 17.793 Å2 / Biso min: 7.57 Å2
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Refinement step | Cycle: final / Resolution: 1.18→55.12 Å
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Refine LS restraints | Type: r_dihedral_angle_2_deg / Dev ideal: 37.847 / Dev ideal target: 24.211 / Number: 19 | ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.18→1.211 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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