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Yorodumi- PDB-6q1a: Inferred intermediate mutant (I-6V) of the human antibody lineage 652 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q1a | |||||||||
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Title | Inferred intermediate mutant (I-6V) of the human antibody lineage 652 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | |||||||||
Authors | McCarthy, K.R. / Harrison, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Affinity maturation in a human humoral response to influenza hemagglutinin. Authors: McCarthy, K.R. / Raymond, D.D. / Do, K.T. / Schmidt, A.G. / Harrison, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q1a.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q1a.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 6q1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/6q1a ftp://data.pdbj.org/pub/pdb/validation_reports/q1/6q1a | HTTPS FTP |
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-Related structure data
Related structure data | 6q0eC 6q0hC 6q0iC 6q0lC 6q0oC 6q18C 6q19C 6q1eC 6q1gC 6q1jC 6q1kC 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: 22930.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) | ||||
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#2: Antibody | Mass: 25773.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 200 mM zinc acetate, 10% (w/v) PEG 8000 100 mM MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.001→43.859 Å / Num. obs: 31446 / % possible obs: 99.89 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06702 / Net I/σ(I): 25.32 |
Reflection shell | Resolution: 2.001→2.073 Å / Rmerge(I) obs: 0.8222 / Num. unique obs: 3073 / CC1/2: 0.795 / % possible all: 99.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→43.859 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.43 Å2 / Biso mean: 42.2094 Å2 / Biso min: 20.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.001→43.859 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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