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- PDB-6tkf: ChiLob 7/4 H2 HC-C225S KappaLC-C214S F(ab')2 -

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Basic information

Entry
Database: PDB / ID: 6tkf
TitleChiLob 7/4 H2 HC-C225S KappaLC-C214S F(ab')2
Components
  • ChiLob 7/4 H2 Heavy chain C225S
  • ChiLob 7/4 H2 Kappa light chain C214S
KeywordsIMMUNE SYSTEM / ---- / antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsOrr, C.M. / Fisher, H. / Tews, I.
CitationJournal: Sci Immunol / Year: 2022
Title: Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility.
Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A. ...Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A.L. / Essex, J.W. / Pearson, A.R. / Cragg, M.S. / Tews, I.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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
HHH: ChiLob 7/4 H2 Heavy chain C225S
LLL: ChiLob 7/4 H2 Kappa light chain C214S


Theoretical massNumber of molelcules
Total (without water)48,5472
Polymers48,5472
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration, native gel electrophoresis, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-27 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.105, 149.105, 45.804
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Antibody ChiLob 7/4 H2 Heavy chain C225S


Mass: 25099.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody ChiLob 7/4 H2 Kappa light chain C214S


Mass: 23447.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 1000, PEG 3350, MPD, MOPS/HEPES-Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.18→129.13 Å / Num. obs: 30651 / % possible obs: 99.9 % / Redundancy: 17.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.023 / Rrim(I) all: 0.1 / Net I/σ(I): 25.1
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2591 / CC1/2: 0.762 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAX

6fax


Resolution: 2.18→48.854 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2394 1490 4.861 %
Rwork0.1961 --
all0.198 --
obs-30650 99.805 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.424 Å20.212 Å20 Å2
2--0.424 Å20 Å2
3----1.375 Å2
Refinement stepCycle: LAST / Resolution: 2.18→48.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 248 3513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133358
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172969
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6474573
X-RAY DIFFRACTIONr_angle_other_deg2.4471.5726949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.4185.329441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.423.841138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21515539
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg45.748154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.679158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024155
X-RAY DIFFRACTIONr_gen_planes_other0.010.02660
X-RAY DIFFRACTIONr_nbd_refined0.1950.2534
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.22713
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21599
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.29
X-RAY DIFFRACTIONr_nbd_other0.210.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.213
X-RAY DIFFRACTIONr_mcbond_it3.2273.8211714
X-RAY DIFFRACTIONr_mcbond_other3.2013.8161712
X-RAY DIFFRACTIONr_mcangle_it4.6525.7082137
X-RAY DIFFRACTIONr_mcangle_other4.6355.7072137
X-RAY DIFFRACTIONr_scbond_it3.9144.1891644
X-RAY DIFFRACTIONr_scbond_other3.9134.191645
X-RAY DIFFRACTIONr_scangle_it5.7326.112433
X-RAY DIFFRACTIONr_scangle_other5.7326.1122434
X-RAY DIFFRACTIONr_lrange_it7.81544.5013628
X-RAY DIFFRACTIONr_lrange_other7.69244.2113567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.2370.4051070.3562085X-RAY DIFFRACTION98.0322
2.237-2.2980.3691000.3452111X-RAY DIFFRACTION99.6844
2.298-2.3650.364980.3372034X-RAY DIFFRACTION100
2.365-2.4370.3291350.2521944X-RAY DIFFRACTION100
2.437-2.5170.311730.2071918X-RAY DIFFRACTION100
2.517-2.6060.257740.1861873X-RAY DIFFRACTION100
2.606-2.7040.286800.2111815X-RAY DIFFRACTION100
2.704-2.8140.249960.2031699X-RAY DIFFRACTION100
2.814-2.9390.229800.1961655X-RAY DIFFRACTION100
2.939-3.0830.239640.1891609X-RAY DIFFRACTION99.9403
3.083-3.2490.241890.1961502X-RAY DIFFRACTION100
3.249-3.4460.224790.1951395X-RAY DIFFRACTION100
3.446-3.6840.241620.1911361X-RAY DIFFRACTION100
3.684-3.9790.209720.1621247X-RAY DIFFRACTION100
3.979-4.3580.179580.1491156X-RAY DIFFRACTION100
4.358-4.8720.161570.1381064X-RAY DIFFRACTION100
4.872-5.6250.187690.158912X-RAY DIFFRACTION100
5.625-6.8850.299360.212790X-RAY DIFFRACTION100
6.885-9.7240.184390.166627X-RAY DIFFRACTION99.8501

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