+Open data
-Basic information
Entry | Database: PDB / ID: 4hk3 | ||||||
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Title | I2 Fab (unbound) from CH65-CH67 Lineage | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment | ||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Schmidt, A.G. / Harrison, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T. ...Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T.B. / Zhang, R. / Moody, M.A. / Haynes, B.F. / Liao, H.X. / Shaw, D.E. / 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 | 4hk3.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hk3.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/4hk3 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hk3 | HTTPS FTP |
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-Related 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: 25771.789 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22695.977 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8N355*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.5 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→50 Å / Num. all: 16978 / Num. obs: 16968 / % possible obs: 100 % / Redundancy: 15 % / Rmerge(I) obs: 0.06 / Χ2: 0.713 / Net I/σ(I): 8.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.964 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7724 / SU ML: 0.35 / σ(F): 1.38 / Phase error: 29.41 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.11 Å2 / ksol: 0.313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.95 Å2 / Biso mean: 47.2921 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: LAST / Resolution: 3→38.964 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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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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