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- PDB-3rfn: Epitope backbone grafting by computational design for improved pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rfn | ||||||
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Title | Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins | ||||||
![]() | BB_1wnu_001 | ||||||
![]() | DE NOVO PROTEIN / protein grafting / flexible backbone design / epitope-scaffold / HIV / immunogen design | ||||||
Function / homology | ![]() Ser-tRNA(Ala) hydrolase activity / aminoacyl-tRNA editing activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Azoitei, M.L. / Ban, Y.A. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Szabo, E. ...Azoitei, M.L. / Ban, Y.A. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Szabo, E. / Pai, E.F. / Schief, W.R. | ||||||
![]() | ![]() Title: Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. Authors: Azoitei, M.L. / Ban, Y.E. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Pai, E.F. / Schief, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.4 KB | Display | ![]() |
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PDB format | ![]() | 30.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
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Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rhuC ![]() 3ri0C ![]() 3rijC ![]() 1wnuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18146.027 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: UNP V22A,L23A,E26A,Y31T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: alaXS, PH0574 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Sequence details | PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-154 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES ...PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-154 WITH A C-TERMINAL EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.8 M NaCl, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 93.2 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2010 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17 Å / Num. all: 15677 / Num. obs: 15316 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rsym value: 0.022 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.44 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.132 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WNU Resolution: 1.8→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→17 Å
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Refine LS restraints |
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