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- PDB-4qks: Crystal Structure of 6xTrp/PV2: de novo designed beta-trefoil arc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qks | ||||||
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Title | Crystal Structure of 6xTrp/PV2: de novo designed beta-trefoil architecture with symmetric primary structure (L22W/L44W/L64W/L85W/L108W/L132W his Primitive Version 2) | ||||||
![]() | DE NOVO PROTEIN 6XTRP/PV2 | ||||||
![]() | DE NOVO PROTEIN / simplified protein design / prebiotic protein / beta-trefoil | ||||||
Function / homology | Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta![]() | ||||||
Biological species | Synthetic (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Longo, L.M. / Tenorio, C.A. / Blaber, M. | ||||||
![]() | ![]() Title: A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding. Authors: Longo, L.M. / Tenorio, C.A. / Kumru, O.S. / Middaugh, C.R. / Blaber, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
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Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 14760.864 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic (others) Description: Synthetic sequence derived from human acidic fibroblast growth factor with symmetric deconstruction method and enriched for pre-biotic amino acids. Plasmid: pET21a(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.4 M (NH4)2SO4, 0.1 M Tris, 0.07 M Li2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2013 / Details: OSMIC CONFOCAL MIRROS |
Radiation | Monochromator: MULTI-LAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 17987 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.076 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.29 Å2 / Biso mean: 26.7528 Å2 / Biso min: 16.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.045 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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