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- PDB-4ub0: New design for monovalent bispecific IgG through cysteine enginee... -

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Basic information

Entry
Database: PDB / ID: 4ub0
TitleNew design for monovalent bispecific IgG through cysteine engineering of the CH1-CL interface
Components
  • IgG1, heavy chain
  • IgG1, light chain
KeywordsIMMUNE SYSTEM / Fab / knobs-into-holes / bispecific
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOganesyan, V.Y. / Dall'Acqua, W.F.
CitationJournal: Mabs / Year: 2015
Title: Improving target cell specificity using a novel monovalent bispecific IgG design.
Authors: Mazor, Y. / Oganesyan, V. / Yang, C. / Hansen, A. / Wang, J. / Liu, H. / Sachsenmeier, K. / Carlson, M. / Gadre, D.V. / Borrok, M.J. / Yu, X.Q. / Dall'Acqua, W. / Wu, H. / Chowdhury, P.S.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: IgG1, heavy chain
L: IgG1, light chain


Theoretical massNumber of molelcules
Total (without water)46,8472
Polymers46,8472
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-25 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.154, 64.045, 82.395
Angle α, β, γ (deg.)90.00, 129.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IgG1, heavy chain


Mass: 23381.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody IgG1, light chain


Mass: 23466.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein @ 19 mg/ml in 10 mM Tris-HCl, pH 8.0, 100 mM NaCl; 0.018 M of each of the following salt solutions: CaCl2, CoCl2, and CdCl2; 18% PEG 3350 and 5% glycerol
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97931 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→53.6 Å / Num. obs: 25434 / % possible obs: 97.4 % / Redundancy: 3.8 % / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.8 / % possible all: 97.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→53.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 19.377 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25202 1277 5.1 %RANDOM
Rwork0.23199 ---
obs0.23308 23745 95.22 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å20.91 Å2
2---3.71 Å20 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.2→53.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 0 19 3281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023344
X-RAY DIFFRACTIONr_bond_other_d0.0010.023055
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.9514557
X-RAY DIFFRACTIONr_angle_other_deg0.66237066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96224.167132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4411514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3563.3441713
X-RAY DIFFRACTIONr_mcbond_other1.3553.3431712
X-RAY DIFFRACTIONr_mcangle_it2.275.0082136
X-RAY DIFFRACTIONr_mcangle_other2.2695.0092137
X-RAY DIFFRACTIONr_scbond_it1.1283.3821631
X-RAY DIFFRACTIONr_scbond_other1.1283.3821631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8625.0252422
X-RAY DIFFRACTIONr_long_range_B_refined4.31425.9043399
X-RAY DIFFRACTIONr_long_range_B_other4.31325.9133400
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 97 -
Rwork0.323 1718 -
obs--94.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.56870.8587-0.3210.84230.02351.9334-0.12440.1188-0.43850.10710.1604-0.20510.20240.4103-0.0360.08990.1293-0.04080.6334-0.09550.0924-25.917.728-20.62
24.47572.5021-0.94811.4663-0.25122.2964-0.08780.11210.2476-0.01820.16860.1133-0.21450.0967-0.08080.14610.112-0.05630.6181-0.00270.0439-39.12829.246-13.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 220
2X-RAY DIFFRACTION2L1 - 214

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