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- PDB-6cr1: adalimumab EFab -

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Basic information

Entry
Database: PDB / ID: 6cr1
Titleadalimumab EFab
Components
  • Heavy chain of adalimumab EFab (VH-IgE CH2)
  • Light chain of adalimumab EFab (VL-IgE CH2)
KeywordsIMMUNE SYSTEM / EFab / IgE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NITRATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 Å
AuthorsArndt, J.W.
CitationJournal: MAbs / Year: 2018
Title: EFab domain substitution as a solution to the light-chain pairing problem of bispecific antibodies.
Authors: Cooke, H.A. / Arndt, J. / Quan, C. / Shapiro, R.I. / Wen, D. / Foley, S. / Vecchi, M.M. / Preyer, M.
History
DepositionMar 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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
Revision 1.4Oct 23, 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
L: Light chain of adalimumab EFab (VL-IgE CH2)
H: Heavy chain of adalimumab EFab (VH-IgE CH2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5195
Polymers48,2892
Non-polymers2303
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-20 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.413, 195.846, 48.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-605-

HOH

21L-616-

HOH

31H-412-

HOH

41H-483-

HOH

51H-508-

HOH

61H-536-

HOH

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Components

#1: Antibody Light chain of adalimumab EFab (VL-IgE CH2)


Mass: 22934.590 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)
#2: Antibody Heavy chain of adalimumab EFab (VH-IgE CH2)


Mass: 25354.104 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)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 15% PEG 3350 and 0.25M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 96198 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.3
Reflection shellResolution: 1.52→1.54 Å / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYL, 2WQR

4nyl

2wqr


Resolution: 1.521→24.898 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.17
RfactorNum. reflection% reflection
Rfree0.1787 4698 5.09 %
Rwork0.1526 --
obs0.1539 92219 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.521→24.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 15 496 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153476
X-RAY DIFFRACTIONf_angle_d1.4274751
X-RAY DIFFRACTIONf_dihedral_angle_d11.1232733
X-RAY DIFFRACTIONf_chiral_restr0.089541
X-RAY DIFFRACTIONf_plane_restr0.013611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5205-1.53780.34721560.30332865X-RAY DIFFRACTION99
1.5378-1.55590.28421750.25742869X-RAY DIFFRACTION100
1.5559-1.57490.27741410.2292846X-RAY DIFFRACTION97
1.5749-1.59480.2171430.21542899X-RAY DIFFRACTION100
1.5948-1.61580.26691460.19572902X-RAY DIFFRACTION99
1.6158-1.63790.2031480.18472863X-RAY DIFFRACTION98
1.6379-1.66130.22181800.18022870X-RAY DIFFRACTION100
1.6613-1.68610.24661440.16872873X-RAY DIFFRACTION98
1.6861-1.71240.16921490.1582863X-RAY DIFFRACTION100
1.7124-1.74050.18721810.14492876X-RAY DIFFRACTION99
1.7405-1.77050.19811560.14742879X-RAY DIFFRACTION100
1.7705-1.80270.19661730.14272901X-RAY DIFFRACTION100
1.8027-1.83740.15221410.13872859X-RAY DIFFRACTION100
1.8374-1.87490.14921720.13452924X-RAY DIFFRACTION99
1.8749-1.91560.18281580.13062882X-RAY DIFFRACTION100
1.9156-1.96010.15921470.11732917X-RAY DIFFRACTION99
1.9601-2.00910.14671720.12222894X-RAY DIFFRACTION100
2.0091-2.06340.17171350.12472923X-RAY DIFFRACTION100
2.0634-2.12410.1431630.1282926X-RAY DIFFRACTION100
2.1241-2.19270.15751400.12532914X-RAY DIFFRACTION100
2.1927-2.2710.16741690.1292918X-RAY DIFFRACTION100
2.271-2.36180.16261450.14322943X-RAY DIFFRACTION100
2.3618-2.46920.17741760.14172927X-RAY DIFFRACTION100
2.4692-2.59930.16131610.1442929X-RAY DIFFRACTION100
2.5993-2.76190.17511640.15532949X-RAY DIFFRACTION100
2.7619-2.97490.20941420.17012972X-RAY DIFFRACTION100
2.9749-3.27370.20181580.16982976X-RAY DIFFRACTION100
3.2737-3.7460.14931560.15043007X-RAY DIFFRACTION100
3.746-4.71430.15791480.14233012X-RAY DIFFRACTION100
4.7143-24.9010.19281590.16813143X-RAY DIFFRACTION99

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