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- PDB-6wgb: Crystal structure of the fab portion of dupilumab -

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Basic information

Entry
Database: PDB / ID: 6wgb
TitleCrystal structure of the fab portion of dupilumab
Components
  • Dupilumab Fab heavy chain
  • Dupilumab Fab light chain
KeywordsIMMUNE SYSTEM / Dupilumab / hIL4R
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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

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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


Theoretical massNumber of molelcules
Total (without water)98,5524
Polymers98,5524
Non-polymers00
Water2,108117
1
A: Dupilumab Fab heavy chain
B: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2762
Polymers49,2762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-21 kcal/mol
Surface area18610 Å2
MethodPISA
2
C: Dupilumab Fab heavy chain
D: Dupilumab Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2762
Polymers49,2762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-20 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.749, 66.293, 135.476
Angle α, β, γ (deg.)90.000, 91.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Dupilumab Fab heavy chain


Mass: 25233.113 Da / Num. of mol.: 2
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: 24042.787 Da / Num. of mol.: 2
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.: 117 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis-Tris pH 5.5, 25% PEG 3350 , 200mM Magnesium Chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.99→67.71 Å / Num. obs: 64075 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 12.7 / Num. measured all: 217034 / Scaling rejects: 112
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.99-2.10.4723012993170.7770.310.5672.499.7
6.3-67.710.029673621240.9980.0190.03532.799.1

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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: self

Resolution: 1.99→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.779 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.193
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 3098 4.8 %RANDOM
Rwork0.2434 ---
obs0.2461 60938 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.14 Å2 / Biso mean: 32.495 Å2 / Biso min: 10.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20.13 Å2
2--0.04 Å20 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 1.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6062 0 0 117 6179
Biso mean---29.45 -
Num. residues----829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126196
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6378438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08624.222225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2915895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8141523
X-RAY DIFFRACTIONr_chiral_restr0.1230.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024613
LS refinement shellResolution: 1.991→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 215 -
Rwork0.332 4497 -
all-4712 -
obs--99.54 %

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