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Yorodumi- PDB-4qgt: The Crystal Structure of Human IgG Fc Domain with Enhanced Aromat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qgt | |||||||||
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Title | The Crystal Structure of Human IgG Fc Domain with Enhanced Aromatic Sequon | |||||||||
Components | Hepatitis B virus receptor binding protein | |||||||||
Keywords | IMMUNE SYSTEM / IgG1 / Immunoglobulin-like beta-sandwich | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | |||||||||
Authors | Kong, L. / Connelly, S.C. / Wilson, I.A. | |||||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Stabilizing the CH2 Domain of an Antibody by Engineering in an Enhanced Aromatic Sequon. Authors: Chen, W. / Kong, L. / Connelly, S. / Dendle, J.M. / Liu, Y. / Wilson, I.A. / Powers, E.T. / Kelly, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qgt.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qgt.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/4qgt ftp://data.pdbj.org/pub/pdb/validation_reports/qg/4qgt | HTTPS FTP |
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-Related structure data
Related structure data | 3aveS 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
#1: Protein | Mass: 26232.773 Da / Num. of mol.: 2 / Mutation: Q295F, Y296A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q6PYX1 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Hepes, 30% PEG 1000 Cryo: +10% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298KK |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / % possible obs: 88.5 % / Redundancy: 2.2 % / Rsym value: 0.082 / Net I/σ(I): 12.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AVE Resolution: 2.99→46.852 Å / SU ML: 0.53 / σ(F): 1.38 / Phase error: 35.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→46.852 Å
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Refine LS restraints |
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LS refinement shell |
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