+Open data
-Basic information
Entry | Database: PDB / ID: 5w6c | ||||||
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Title | UCA Fab (unbound) from 6649 Lineage | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / FAB / Influenza H1N1 | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.634 Å | ||||||
Authors | Raymond, D.D. / Harrison, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Authors: Raymond, D.D. / Bajic, G. / Ferdman, J. / Suphaphiphat, P. / Settembre, E.C. / Moody, M.A. / 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 | 5w6c.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w6c.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w6c_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 5w6c_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 5w6c_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 5w6c_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6c ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6c | HTTPS FTP |
-Related structure data
Related structure data | 5w6gC 3h42S 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: Antibody | Mass: 25308.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2B6 |
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#2: Antibody | Mass: 22847.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 26% PEG2000 MME, 150 mM ammonium sulfate, 100 mM sodium acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 293.15 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.999919 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999919 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.63→46.116 Å / Num. obs: 52465 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.629 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 1.048 / Net I/σ(I): 27.48 / Num. measured all: 347776 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H42 Resolution: 1.634→46.116 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.68 Å2 / Biso mean: 18.8155 Å2 / Biso min: 7.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.634→46.116 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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