+Open data
-Basic information
Entry | Database: PDB / ID: 5dvm | ||||||
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Title | Fc Design 20.8.37 B chain homodimer E357D/S364R/Y407A | ||||||
Components |
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Keywords | IMMUNE SYSTEM / head-to-tail homodimer / Immunoglobulin / Fc | ||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å | ||||||
Model details | Design XXX | ||||||
Authors | Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. ...Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. / Fitchett, J.R. / Gutierrez, B. / Hendle, J. / Demarest, S.J. / Kuhlman, B. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Computationally Designed Bispecific Antibodies using Negative State Repertoires. Authors: Leaver-Fay, A. / Froning, K.J. / Atwell, S. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Hassanali, S. / Chamberlain, A.K. / Fitchett, J.R. / Demarest, S.J. / Kuhlman, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dvm.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dvm.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/5dvm ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dvm | HTTPS FTP |
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-Related structure data
Related structure data | 5di8C 5dj0C 5dj2C 5dj6C 5dj8C 5djaC 5djcC 5djdC 5djxC 5djyC 5djzC 5dk0C 5dk2C 5dvkC 5dvlC 5dvnC 5dvoC 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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Unit cell |
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-Components
#1: Protein | Mass: 25577.012 Da / Num. of mol.: 1 / Fragment: UNP residues 104-330 / Mutation: E357D, S364R, Y407A Source method: isolated from a genetically manipulated source Details: transient expression / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857 |
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#2: Protein/peptide | Mass: 1533.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.27 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: 100mM Sodium Cacodylate pH 6.5 + 20% PEG 8K + 200mM Magnesium Acetate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 193 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2014 / Details: Diamond (111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→30 Å / Num. obs: 8056 / % possible obs: 98.7 % / Redundancy: 5.7 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Rsym value: 0.136 / Net I/av σ(I): 4.279 / Net I/σ(I): 7.9 / Num. measured all: 45883 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.583 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.5 Å2 / Biso mean: 69.424 Å2 / Biso min: 32.96 Å2
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Refinement step | Cycle: final / Resolution: 2.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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