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- PDB-6tke: ChiLob 7/4 H2 HC-C224S Kappa LC-C214S F(ab')2 -

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Basic information

Entry
Database: PDB / ID: 6tke
TitleChiLob 7/4 H2 HC-C224S Kappa LC-C214S F(ab')2
Components
  • ChiLob 7/4 H2 heavy chain C224S
  • ChiLob 7/4 H2 kappa chain C214S
KeywordsIMMUNE SYSTEM / ----
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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 16, 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
HHH: ChiLob 7/4 H2 heavy chain C224S
LLL: ChiLob 7/4 H2 kappa chain C214S


Theoretical massNumber of molelcules
Total (without water)48,5472
Polymers48,5472
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-28 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.204, 148.204, 45.652
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 C224S


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 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.: 121 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 4000, cacodylate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.755 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.755 Å / Relative weight: 1
ReflectionResolution: 2.35→128.35 Å / Num. obs: 22283 / % possible obs: 92.4 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.036 / Rrim(I) all: 0.129 / Net I/σ(I): 14.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1933 / CC1/2: 0.373 / Rpim(I) all: 0.771 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD
Starting model: 6FAX

6fax


Resolution: 2.35→128.348 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.172 / Average fsc free: 0.8619 / Average fsc work: 0.8899 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.241
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2453 1092 4.901 %
Rwork0.1918 21189 -
all0.194 --
obs-22281 92.097 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.985 Å2
Baniso -1Baniso -2Baniso -3
1-0.153 Å20.076 Å20 Å2
2--0.153 Å20 Å2
3----0.496 Å2
Refinement stepCycle: LAST / Resolution: 2.35→128.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 121 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133341
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172948
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6464546
X-RAY DIFFRACTIONr_angle_other_deg2.441.5716900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6115423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55624.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3615539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.654158
X-RAY DIFFRACTIONr_chiral_restr0.060.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023708
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02652
X-RAY DIFFRACTIONr_nbd_refined0.1930.2512
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.22576
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21545
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.28
X-RAY DIFFRACTIONr_nbd_other0.1830.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2920.28
X-RAY DIFFRACTIONr_mcbond_it4.0255.2991707
X-RAY DIFFRACTIONr_mcbond_other4.0255.2951705
X-RAY DIFFRACTIONr_mcangle_it6.087.9262125
X-RAY DIFFRACTIONr_mcangle_other6.087.9262125
X-RAY DIFFRACTIONr_scbond_it4.4655.8311634
X-RAY DIFFRACTIONr_scbond_other4.4635.8331635
X-RAY DIFFRACTIONr_scangle_it6.8888.5172421
X-RAY DIFFRACTIONr_scangle_other6.8878.5182422
X-RAY DIFFRACTIONr_lrange_it9.26860.5923444
X-RAY DIFFRACTIONr_lrange_other9.26760.6113445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.35-2.4110.382810.33813570.34117560.6920.74681.89070.34
2.411-2.4770.32740.32213670.32217140.7170.76684.07230.321
2.477-2.5490.382690.31313560.31616990.7430.76583.87290.308
2.549-2.6270.354730.29513490.29816230.7870.80787.61550.287
2.627-2.7130.326800.26312940.26715730.8420.84987.3490.246
2.713-2.8090.312630.23612960.23915430.8430.88688.07520.219
2.809-2.9150.323460.2212820.22314740.8590.90590.0950.197
2.915-3.0340.226600.20112720.20214410.9010.92192.43580.18
3.034-3.1680.224730.19611970.19713610.9240.93393.31370.178
3.168-3.3230.296620.21211810.21513090.8850.92794.9580.196
3.323-3.5030.253590.19811630.20112610.9180.94196.90720.185
3.503-3.7150.238570.19511020.19711660.9330.95199.39970.185
3.715-3.9710.211480.16510640.16711130.9340.95999.91010.157
3.971-4.2890.167380.15610140.15710520.960.9621000.149
4.289-4.6980.238450.149300.1449750.9420.9651000.135
4.698-5.2510.205490.1388060.1428550.9580.9661000.134
5.251-6.0620.231450.1637350.1677800.9460.961000.159
6.062-7.420.236390.1856230.1886620.9370.9521000.179
7.42-10.4770.213200.1525020.1545220.9620.9721000.155
10.477-128.3480.17110.2382990.2353100.9710.9341000.235

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