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Yorodumi- PDB-3p6i: Crystal structure of Symfoil-4T Permutation #2: de novo designed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p6i | ||||||
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Title | Crystal structure of Symfoil-4T Permutation #2: 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Blaber, M. / Lee, J. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p6i.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p6i.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3p6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/3p6i ftp://data.pdbj.org/pub/pdb/validation_reports/p6/3p6i | HTTPS FTP |
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-Related 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: 15849.183 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: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2M ammonium sulfate, 0.2M Li2SO4, 0.1M Tris, 17mg/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: NSLS / Beamline: X25 / Wavelength: 1.075 Å |
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: 1.32→50 Å / Num. all: 27352 / Num. obs: 25102 / % possible obs: 91.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 35.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 106.5 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1301 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→36.797 Å / σ(F): 4.48 / Stereochemistry target values: ML
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.32→36.797 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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