+Open data
-Basic information
Entry | Database: PDB / ID: 6iqg | ||||||||||||
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Title | X-ray crystal structure of Fc and peptide complex | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fc / Complex | ||||||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.998 Å | ||||||||||||
Authors | Adachi, M. / Ito, Y. | ||||||||||||
Citation | Journal: Bioconjug. Chem. / Year: 2019 Title: Site-Specific Chemical Conjugation of Antibodies by Using Affinity Peptide for the Development of Therapeutic Antibody Format. Authors: Kishimoto, S. / Nakashimada, Y. / Yokota, R. / Hatanaka, T. / Adachi, M. / Ito, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iqg.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iqg.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 6iqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iqg_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6iqg_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6iqg_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6iqg_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqg ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqg | HTTPS FTP |
-Related structure data
Related structure data | 6iqhC 1dn2S 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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Unit cell |
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-Components
#1: Antibody | Mass: 23788.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5 #2: Protein/peptide | Mass: 1982.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CL / | #5: 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: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: PEG 3350, KI |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.998→44.22 Å / Num. obs: 10959 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / Num. unique obs: 1071 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1DN2 Resolution: 2.998→35.034 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.998→35.034 Å
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Refine LS restraints |
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LS refinement shell |
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