+Open data
-Basic information
Entry | Database: PDB / ID: 5y2k | ||||||
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Title | A human antibody AF4H1L1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / influenza virus / H3-clade / neutralizing antibody / H7N9-infected patient / next generation sequencing | ||||||
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: 2.1 Å | ||||||
Authors | Xiao, H. / Qi, J. / Gao, F.G. | ||||||
Citation | Journal: To Be Published Title: An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins Authors: Xiao, H. / Qi, J. / Gao, F.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y2k.cif.gz | 657.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y2k.ent.gz | 548.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y2k ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y2k | HTTPS FTP |
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-Related structure data
Related structure data | 5y2lC 5y2mC 4py8S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24977.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) #2: Antibody | Mass: 23417.818 Da / Num. of mol.: 4 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: 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: 2.72 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Bicine pH9.0, 2% v/v 1,4-Dioxane, 10% w/v PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 118899 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.1→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 11093 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PY8 Resolution: 2.1→41.63 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.1→41.63 Å
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