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- PDB-5vr9: CH1/Ckappa Fab based on Matuzumab -

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Basic information

Entry
Database: PDB / ID: 5vr9
TitleCH1/Ckappa Fab based on Matuzumab
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 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
IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 10, 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CH1/Ckappa Fab heavy chain
B: CH1/Ckappa Fab light chain
H: CH1/Ckappa Fab heavy chain
L: CH1/Ckappa Fab light chain


Theoretical massNumber of molelcules
Total (without water)94,8534
Polymers94,8534
Non-polymers00
Water6,575365
1
A: CH1/Ckappa Fab heavy chain
B: CH1/Ckappa Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4272
Polymers47,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-22 kcal/mol
Surface area19510 Å2
MethodPISA
2
H: CH1/Ckappa Fab heavy chain
L: CH1/Ckappa Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4272
Polymers47,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-21 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.046, 152.046, 220.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11H-369-

HOH

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Components

#1: Antibody CH1/Ckappa Fab heavy chain


Mass: 24190.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMX6
#2: Antibody CH1/Ckappa Fab light chain


Mass: 23235.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q7Z3Y4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: see publication for details

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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 9, 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: 2.15→30 Å / Num. obs: 70553 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.6
Reflection shellResolution: 2.15→2.26 Å / Redundancy: 12 % / Rmerge(I) obs: 0.551 / Num. unique obs: 10174 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c08

3c08


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.322 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.171 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 3533 5 %RANDOM
Rwork0.2098 ---
obs0.2116 66523 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 183.57 Å2 / Biso mean: 42.763 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 0 370 6832
Biso mean---43.11 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026669
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9379107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77424.806258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8941516
X-RAY DIFFRACTIONr_chiral_restr0.0750.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215051
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 256 -
Rwork0.269 4848 -
all-5104 -
obs--100 %

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