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- PDB-6wgk: Fab portion of dupilumab with Crystal Kappa design and intrachain... -

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Basic information

Entry
Database: PDB / ID: 6wgk
TitleFab portion of dupilumab with Crystal Kappa design and intrachain disulfide
Components
  • Dupilumab Fab heavy chain
  • Dupilumab Fab light chain
KeywordsIMMUNE SYSTEM / Dupilumab / hIL4R
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDruzina, Z. / Atwell, S. / Pustilnik, A. / Antonysamy, S. / Ho, C. / Lieu, R. / Hendle, J. / Benach, J. / Wang, J.
CitationJournal: Plos One / Year: 2020
Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
History
DepositionApr 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dupilumab Fab heavy chain
B: Dupilumab Fab light chain
C: Dupilumab Fab heavy chain
D: Dupilumab Fab light chain
E: Dupilumab Fab heavy chain
F: Dupilumab Fab light chain
G: Dupilumab Fab heavy chain
H: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)196,1348
Polymers196,1348
Non-polymers00
Water14,250791
1
A: Dupilumab Fab heavy chain
B: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,0342
Polymers49,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-22 kcal/mol
Surface area19320 Å2
MethodPISA
2
C: Dupilumab Fab heavy chain
D: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,0342
Polymers49,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area19200 Å2
MethodPISA
3
E: Dupilumab Fab heavy chain
F: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,0342
Polymers49,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-25 kcal/mol
Surface area19350 Å2
MethodPISA
4
G: Dupilumab Fab heavy chain
H: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,0342
Polymers49,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-24 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.156, 79.265, 109.556
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Dupilumab Fab heavy chain


Mass: 25230.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Dupilumab Fab light chain


Mass: 23803.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris HCl pH 8.5, 20% PEG MME 2K , 200mM Trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.62→109.5 Å / Num. obs: 225219 / % possible obs: 95.5 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 12.6 / Num. measured all: 809633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.62-1.713.60.454119674328950.8610.2760.5332.595.7
5.13-109.53.50.0412576272900.9970.0250.04827.594.5

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WGB

6wgb


Resolution: 1.62→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.087 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 11284 5 %RANDOM
Rwork0.2097 ---
obs0.211 213881 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.12 Å2 / Biso mean: 28.25 Å2 / Biso min: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å20.62 Å2
2--1.11 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.62→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12816 0 0 791 13607
Biso mean---32.92 -
Num. residues----1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01213297
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.63818184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0065.0111790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58623.903497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.297151994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1151559
X-RAY DIFFRACTIONr_chiral_restr0.080.21799
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029964
LS refinement shellResolution: 1.621→1.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 806 -
Rwork0.295 15794 -
all-16600 -
obs--95.53 %

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