+Open data
-Basic information
Entry | Database: PDB / ID: 5nb5 | ||||||
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Title | Principles for computational design of antibodies | ||||||
Components | (design of antibodies) x 2 | ||||||
Keywords | IMMUNE SYSTEM / antibodies | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Dym, O. / Fleishman, S.J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Principles for computational design of binding antibodies. Authors: Baran, D. / Pszolla, M.G. / Lapidoth, G.D. / Norn, C. / Dym, O. / Unger, T. / Albeck, S. / Tyka, M.D. / Fleishman, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nb5.cif.gz | 335.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nb5.ent.gz | 277.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nb5_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 5nb5_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 5nb5_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 5nb5_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nb5 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nb5 | HTTPS FTP |
-Related structure data
Related structure data | 5nbiC 2hffS 3qq9S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Antibody | Mass: 24056.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 23472.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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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: 2.9 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M (NH4)2SO4 0.05M Tris pH=8.5 12.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 3→90 Å / Num. obs: 21280 / % possible obs: 93 % / Redundancy: 4.2 % / Rsym value: 0.195 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2854 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QQ9, 2HFF Resolution: 3→90 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.844 / SU B: 48.33 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.253 Å2
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Refinement step | Cycle: 1 / Resolution: 3→90 Å
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Refine LS restraints |
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