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Yorodumi- PDB-3rfs: Design of a binding scaffold based on variable lymphocyte recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rfs | ||||||
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Title | Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering | ||||||
Components | Internalin B, repeat modules, Variable lymphocyte receptor B | ||||||
Keywords | PROTEIN BINDING / LRR / plasma | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) Eptatretus burgeri (inshore hagfish) synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kim, H.J. / Cheong, H.K. / Jeon, Y.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering Authors: Lee, S.C. / Park, K. / Han, J. / Lee, J.J. / Kim, H.J. / Hong, S. / Heu, W. / Kim, Y.J. / Ha, J.S. / Lee, S.G. / Cheong, H.K. / Jeon, Y.H. / Kim, D. / Kim, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rfs.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rfs.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/3rfs ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rfs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30425.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chimera of Internalin B, repeat modules, Variable lymphocyte receptor B Source: (gene. exp.) Listeria monocytogenes (bacteria), (gene. exp.) Eptatretus burgeri (inshore hagfish), (gene. exp.) synthetic (others) Strain: 08-5923 / Production host: Escherichia coli (E. coli) / References: UniProt: D2P9A6, UniProt: Q4G1L3 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE RESIDUE 66-179 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MOLDUES IS ...THE RESIDUE 66-179 REPRESENTS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.1M Tris-HCl, 30%(w/v) polyethylene glycol 4000, 0.2M magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.83 Å / Num. all: 52267 / Num. obs: 49492 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.83 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.288 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.544 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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