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Yorodumi- PDB-5fuz: Extending the half-life of a Fab fragment through generation of a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fuz | ||||||
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Title | Extending the half-life of a Fab fragment through generation of a humanised anti-Human Serum Albumin (HSA) Fv domain: an investigation into the correlation between affinity and serum half-life | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTI-ALBUMIN / FAB FRAGMENT / SERUM HALF-LIFE / FCRN / HUMAN SERUM ALBUMIN | ||||||
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: 2.68 Å | ||||||
Authors | Adams, R. / Ceska, T. | ||||||
Citation | Journal: Mabs / Year: 2016 Title: Extending the Half-Life of a Fab Fragment Through Generation of a Humanized Anti-Human Serum Albumin Fv Domain: An Investigation Into the Correlation between Affinity and Serum Half-Life. Authors: Adams, R. / Griffin, L. / Compson, J.E. / Jairaj, M. / Baker, T. / Ceska, T. / West, S. / Zaccheo, O. / Dave, E. / Lawson, A.D.G. / Humphreys, D.P. / Heywood, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fuz.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fuz.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fuz ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fuz | 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: 24900.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED RABBIT IGG FAB FRAGMENT / Cell line: CHINESE HAMSTER OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) |
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#2: Antibody | Mass: 23419.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED RABBIT IGG FAB FRAGMENT / Cell line: CHINESE HAMSTER OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) |
#3: Water | ChemComp-HOH / |
Sequence details | IN-HOUSE DISCOVERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Details: 2 M DL-MALIC ACID |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→30 Å / Num. obs: 18151 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 21.5 % / Biso Wilson estimate: 44.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.68→2.82 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 10.1 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE FAB Resolution: 2.68→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAIN L RESIDUE 217, AND CHAIN H RESIDUES 223-233 ARE DISORDERED
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Solvent computation | Bsol: 24.7299 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3588 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.78 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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