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- PDB-3p6j: Crystal structure of Symfoil-4T Permutation #3: de novo designed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p6j | ||||||
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Title | Crystal structure of Symfoil-4T Permutation #3: de novo designed beta-trefoil architecture with symmetric primary structure | ||||||
![]() | de novo designed beta-trefoil architecture with symmetric primary structure | ||||||
![]() | DE NOVO PROTEIN / beta-trefoil | ||||||
Function / homology | Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blaber, M. / Lee, J. | ||||||
![]() | ![]() Title: Permutations study of de novo designed symmetric beta-trefoil architecture Authors: Blaber, M. / Lee, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 420 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.9 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: 15877.192 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Circularly permuted synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence adopts a beta-trefoil ...Details: Circularly permuted synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence adopts a beta-trefoil architecture with symmetric primary structure. |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.0M sodium citrate, 0.1M sodium cacodylate, 10mg/mL protein concentration, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 36190 / Num. obs: 33256 / % possible obs: 91.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 12 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 61.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1739 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.109 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.35→36.375 Å
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Refine LS restraints |
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LS refinement shell |
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