+Open data
-Basic information
Entry | Database: PDB / ID: 6ifj | |||||||||
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Title | Structure of bispecific Fc | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Qian, X. / Lescar, J. / Sasisekahran, R. | |||||||||
Citation | Journal: To Be Published Title: Structure of bsfc at 2.4 Angstroms resolution Authors: Qian, X. / Lescar, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ifj.cif.gz | 216.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ifj.ent.gz | 170.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ifj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/6ifj ftp://data.pdbj.org/pub/pdb/validation_reports/if/6ifj | HTTPS FTP |
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-Related structure data
Related structure data | 4byhS S: Starting model for refinement |
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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
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 26154.666 Da / Num. of mol.: 1 / Mutation: E357K,K409R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 |
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#2: Antibody | Mass: 26126.520 Da / Num. of mol.: 1 / Mutation: K370E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 |
-Protein/peptide / Sugars , 2 types, 4 molecules CD
#3: Protein/peptide | Mass: 1533.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 355 molecules
#5: Chemical | ChemComp-GOL / #6: 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: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion Details: 0.1M Hepes, pH7.5, 12%(w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.954 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.11 Å / Num. obs: 23965 / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3485 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4byh Resolution: 2.4→37.18 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.335 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.23
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Displacement parameters | Biso mean: 43.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→37.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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