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Yorodumi- PDB-6iqh: X-ray crystal structure of covalent-bonded complex of Fc and peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iqh | ||||||||||||
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Title | X-ray crystal structure of covalent-bonded complex of Fc and peptide | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fc / Complex | ||||||||||||
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 / FOURIER SYNTHESIS / Resolution: 2.999 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 | 6iqh.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iqh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6iqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqh ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqh | HTTPS FTP |
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-Related structure data
Related structure data | 6iqgC 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: 2063.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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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: 3.18 Å3/Da / Density % sol: 61.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.1 M CHES pH 10.0, 0.3M NaCl, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.999→44.1 Å / Num. obs: 12253 / % possible obs: 98.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1158 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1DN2 Resolution: 2.999→44.1 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.999→44.1 Å
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Refine LS restraints |
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LS refinement shell |
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