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Yorodumi- PDB-3o4c: Crystal structure of Symfoil-4V: de novo designed beta-trefoil ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o4c | ||||||
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Title | Crystal structure of Symfoil-4V: de novo designed beta-trefoil architecture with symmetric primary structure | ||||||
Components | de novo designed beta-trefoil architecture with symmetric primary structure | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lee, J. / Blaber, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Authors: Lee, J. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o4c.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o4c.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 3o4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4c ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4c | HTTPS FTP |
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-Related structure data
Related structure data | 3o49C 3o4aC 3o4bC 3o4dC 3ogfC 3ol0C 3o4e C: citing same article (ref.) |
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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 | Mass: 15869.304 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 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 ...Details: 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. Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | ChemComp-TRS / | ||||
#3: Chemical | #4: Chemical | #5: 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: 1.84 Å3/Da / Density % sol: 33.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M ammonium sulfate, 0.2M Li2SO4, 0.1M Tris, 15mg/mL protein concentration, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 11947 / Num. obs: 11700 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 50.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 8.1 / Num. unique all: 594 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.51 Å / SU ML: 0.23 / σ(F): 0.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.056 Å2 / ksol: 0.402 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→45.51 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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