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Yorodumi- PDB-6chf: Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6chf | |||||||||
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Title | Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal form 1) | |||||||||
Components | Uncharacterized protein DKFZp686C11235 | |||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin / IgG1 / immunoglobulin-like beta sandwich / FC fragment / LALA mutation | |||||||||
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 / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Gohain, N. / Tolbert, W.D. / Pazgier, M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2020 Title: Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fc gamma Receptor Binding. Authors: Orlandi, C. / Deredge, D. / Ray, K. / Gohain, N. / Tolbert, W. / DeVico, A.L. / Wintrode, P. / Pazgier, M. / Lewis, G.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6chf.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6chf.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 6chf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6chf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6chf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6chf_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 6chf_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6chf ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6chf | HTTPS FTP |
-Related structure data
Related structure data | 6cjcC 6cjxC 3aveS 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: Protein | Mass: 24149.293 Da / Num. of mol.: 2 / Mutation: L234A L235A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG MME 5,000 0.1 M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015 / Details: Flat SI Rh coated M0 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 18034 / % possible obs: 89.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.171 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.6 / Num. unique obs: 741 / CC1/2: 0.604 / Rpim(I) all: 0.469 / % possible all: 74.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AVE Resolution: 2.4→46.055 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 31.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.055 Å
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Refine LS restraints |
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LS refinement shell |
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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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