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Yorodumi- PDB-4n9g: Crystal Structure of a Computationally Designed RSV-Presenting Ep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n9g | ||||||
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Title | Crystal Structure of a Computationally Designed RSV-Presenting Epitope Scaffold And Its Elicited Antibody 17HD9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Hairpin / Epitope Scaffold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Macaca mulatta (Rhesus monkey) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Carrico, C.T.D. / Strong, R.K. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Proof of principle for epitope-focused vaccine design. Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. ...Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. / Chen, M. / Macpherson, S. / Serra, A.M. / Adachi, Y. / Holmes, M.A. / Li, Y. / Klevit, R.E. / Graham, B.S. / Wyatt, R.T. / Baker, D. / Strong, R.K. / Crowe, J.E. / Johnson, P.R. / Schief, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n9g.cif.gz | 697.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n9g.ent.gz | 580.2 KB | Display | PDB format |
PDBx/mmJSON format | 4n9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n9g ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n9g | HTTPS FTP |
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-Related structure data
Related structure data | 4jlrC 4l8iC 3eo9S 3q6gS 3qhzS 3sobS S: Starting model for refinement 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Antibody | Mass: 24461.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pHLsec / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) #2: Antibody | Mass: 23512.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pHLsec / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) #3: Protein | Mass: 14450.532 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Gene: Computationally designed variant of Ribosomal Recycling Factor Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 #4: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2013 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.75 Å / Num. all: 78170 / Num. obs: 76354 / % possible obs: 97.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.4 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS ...Starting model: 17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED Resolution: 2.5→48.75 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.829 / SU B: 23.784 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.336 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.108 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.75 Å
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Refine LS restraints |
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