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- PDB-5fuz: Extending the half-life of a Fab fragment through generation of a... -

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Basic information

Entry
Database: PDB / ID: 5fuz
TitleExtending 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
  • 645 FAB, HEAVY CHAIN
  • 645 FAB, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTI-ALBUMIN / FAB FRAGMENT / SERUM HALF-LIFE / FCRN / HUMAN SERUM ALBUMIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsAdams, R. / Ceska, T.
CitationJournal: 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
DepositionFeb 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 645 FAB, HEAVY CHAIN
L: 645 FAB, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)48,3212
Polymers48,3212
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-27.4 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.210, 111.210, 89.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody 645 FAB, HEAVY CHAIN


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)
#2: Antibody 645 FAB, LIGHT CHAIN


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 / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN-HOUSE DISCOVERED FAB

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 2 M DL-MALIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.68→2.82 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 10.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 1790 9.8 %RANDOM
Rwork0.2119 ---
obs0.2119 18142 99.4 %-
Solvent computationBsol: 24.7299 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.772 Å20 Å20 Å2
2--5.772 Å20 Å2
3----11.545 Å2
Refine analyzeLuzzati coordinate error obs: 0.3588 Å
Refinement stepCycle: LAST / Resolution: 2.68→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 0 37 3336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006779
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.42054
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.68→2.78 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 190 11.9 %
Rwork0.303 1599 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR PROTEIN_REP.PARAMA
X-RAY DIFFRACTION2CNS_TOPPAR DNA-RNA_REP.PARAMA
X-RAY DIFFRACTION3CNS_TOPPAR WATER_REP.PARAMA
X-RAY DIFFRACTION4CNS_TOPPAR ION.PARAMA
X-RAY DIFFRACTION5CNS_TOPPAR CARBOHYDRATE.PARAMA

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