+Open data
-Basic information
Entry | Database: PDB / ID: 7lf9 | ||||||
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Title | Structure of Hyperglycosylated Human IgG1 Fc (Fc329) | ||||||
Components | IgG1 Fc (Fc329) | ||||||
Keywords | SIGNALING PROTEIN / Effector / IgG / Antibody / Fc | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fields, J.K. / Sundberg, E.J. | ||||||
Citation | Journal: To Be Published Title: Silent Antibodies: Generation of Hyperglycosylated FCs to Ablate Effector Functions Authors: Fields, J.K. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lf9.cif.gz | 217.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lf9.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 7lf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lf9 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lf9 | HTTPS FTP |
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-Related structure data
Related structure data | 7lblC 7lf5C 7lfnC 4cdhS 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
-Antibody / Non-polymers , 2 types, 27 molecules AB
#1: Antibody | Mass: 26252.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7 #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 | ||
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#3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 | ||
#4: Sugar | #5: Sugar | ChemComp-NAG / | |
-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: CRYSTALS GROWN BY MIXING 1 UL OF FC329 (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.1M HEPES pH 6.5, 12.571% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.03319 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28.64 Å / Num. obs: 28367 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 47.72 Å2 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.028 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2429 / Rpim(I) all: 0.028 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4cdh Resolution: 2.2→28.64 Å / SU ML: 0.2653 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1846 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→28.64 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.0538379736 Å / Origin y: 0.995734289445 Å / Origin z: 25.691706963 Å
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Refinement TLS group | Selection details: all |