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- PDB-5vsi: CH1/Ckappa Fab mutant 15.1 -

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Basic information

Entry
Database: PDB / ID: 5vsi
TitleCH1/Ckappa Fab mutant 15.1
Components
  • CH1/Ckappa Fab heavy chain
  • CH1/Ckappa Fab light chain
KeywordsIMMUNE SYSTEM / bispecific antibody / computational design / heavy chain/light chain interface / CH1/Ckappa interface
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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
IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsHendle, J.
CitationJournal: Protein Sci. / Year: 2017
Title: Computational design of a specific heavy chain/ kappa light chain interface for expressing fully IgG bispecific antibodies.
Authors: Froning, K.J. / Leaver-Fay, A. / Wu, X. / Phan, S. / Gao, L. / Huang, F. / Pustilnik, A. / Bacica, M. / Houlihan, K. / Chai, Q. / Fitchett, J.R. / Hendle, J. / Kuhlman, B. / Demarest, S.J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: CH1/Ckappa Fab heavy chain
L: CH1/Ckappa Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84111
Polymers47,1122
Non-polymers7299
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Fab heterodimer of heavy and light chain
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-45 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.279, 60.610, 86.241
Angle α, β, γ (deg.)90.000, 100.590, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-301-

SO4

21H-302-

SO4

31H-519-

HOH

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Components

#1: Antibody CH1/Ckappa Fab heavy chain


Mass: 23780.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMX6
#2: Antibody CH1/Ckappa Fab light chain


Mass: 23331.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q7Z3Y4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: see publication

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2015
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.51→19.9 Å / Num. obs: 73293 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.4
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10568 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VR9

5vr9


Resolution: 1.51→19.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.791 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 3636 5 %RANDOM
Rwork0.1936 ---
obs0.1953 69649 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.33 Å2 / Biso mean: 20.19 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0.68 Å2
2---0.18 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.51→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 41 407 3730
Biso mean--48.61 29.21 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023580
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9494918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19524.643140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45115556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7841511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212708
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 279 -
Rwork0.317 5023 -
all-5302 -
obs--96.63 %

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