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- PDB-5gjs: Crystal structure of H1 hemagglutinin from A/California/04/2009 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gjs | |||||||||
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Title | Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1 | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, W. / Zhang, T. / Ding, J. | |||||||||
![]() | ![]() Title: Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses Authors: Wang, W. / Sun, X. / Li, Y. / Su, J. / Ling, Z. / Zhang, T. / Wang, F. / Zhang, H. / Chen, H. / Ding, J. / Sun, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.8 KB | Display | ![]() |
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PDB format | ![]() | 286.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5gjtC ![]() 3lzjS ![]() 3nfsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 36525.242 Da / Num. of mol.: 1 / Fragment: UNP residues 18-344 / Mutation: G212C, R227C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 20842.113 Da / Num. of mol.: 1 / Fragment: neutralizing antibody 3E1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23483.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Antibody | Mass: 23663.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() |
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#6: Sugar | ChemComp-NAG / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.89 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES and 16% PEG 550MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→50 Å / Num. obs: 25201 / % possible obs: 93.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3LZJ, 3NFS Resolution: 2.9→47.98 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.814 / SU B: 48.675 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Details: U VALUES : WITH TLS ADDED,
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.37 Å2 / Biso mean: 51.878 Å2 / Biso min: 20.67 Å2
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Refinement step | Cycle: final / Resolution: 2.9→47.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.901→2.977 Å / Total num. of bins used: 20
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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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