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- PDB-6tkd: ChiLob 7/4 H2 HC-C228S F(ab')2 -

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Basic information

Entry
Database: PDB / ID: 6tkd
TitleChiLob 7/4 H2 HC-C228S F(ab')2
Components
  • Chilob 7/4 H2 heavy chain C228S
  • Chilob 7/4 H2 kappa chain
KeywordsIMMUNE SYSTEM / ----
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Nov 13, 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 C228S
LLL: Chilob 7/4 H2 kappa chain


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water7,224401
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 area3610 Å2
ΔGint-27 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.021, 148.021, 46.139
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11HHH-392-

HOH

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Components

#1: Antibody Chilob 7/4 H2 heavy chain C228S


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


Mass: 23463.865 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.: 401 / 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: 3.05 Å3/Da / Density % sol: 59.64 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→128.19 Å / Num. obs: 45431 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2857 / CC1/2: 0.768 / Rpim(I) all: 0.32

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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: 1.9→128.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.174 / Average fsc free: 0.9341 / Average fsc work: 0.9457 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2064 2214 4.875 %
Rwork0.1726 43199 -
all0.174 --
obs-45413 98.967 %
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: 27.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å20.009 Å20 Å2
2--0.017 Å20 Å2
3----0.056 Å2
Refinement stepCycle: LAST / Resolution: 1.9→128.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 401 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133609
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173134
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6454942
X-RAY DIFFRACTIONr_angle_other_deg2.5771.5687359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8915477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43324.359156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26115580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.972159
X-RAY DIFFRACTIONr_chiral_restr0.080.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024138
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02717
X-RAY DIFFRACTIONr_nbd_refined0.1890.2554
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22804
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21626
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2355
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.213
X-RAY DIFFRACTIONr_nbd_other0.1840.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.223
X-RAY DIFFRACTIONr_mcbond_it2.6322.7361853
X-RAY DIFFRACTIONr_mcbond_other2.6312.7361852
X-RAY DIFFRACTIONr_mcangle_it3.714.0752339
X-RAY DIFFRACTIONr_mcangle_other3.7094.0752340
X-RAY DIFFRACTIONr_scbond_it3.3773.0971756
X-RAY DIFFRACTIONr_scbond_other3.3763.0981757
X-RAY DIFFRACTIONr_scangle_it5.044.4892600
X-RAY DIFFRACTIONr_scangle_other5.0394.4892601
X-RAY DIFFRACTIONr_lrange_it7.04632.6423931
X-RAY DIFFRACTIONr_lrange_other6.84232.1023831
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
1.9-1.9490.221620.21331090.21333630.9190.91497.26440.216
1.949-2.0030.2461470.230770.20233210.9050.9297.07920.202
2.003-2.0610.2211740.18529550.18731460.9210.93599.45960.185
2.061-2.1240.2231180.17829380.1831100.9270.93898.26370.177
2.124-2.1940.2831510.17528240.1830070.9030.94198.93580.173
2.194-2.2710.2171160.17327700.17529020.9390.94699.44870.171
2.271-2.3570.2071350.17226430.17328110.940.94898.8260.17
2.357-2.4530.2591210.1725700.17427190.9160.94198.97020.167
2.453-2.5620.2281390.16724510.1726060.9290.95299.3860.163
2.562-2.6870.2191240.15723440.1624720.940.95899.83820.155
2.687-2.8320.221170.15922220.16223560.9430.95699.27840.158
2.832-3.0040.211050.1721240.17222440.950.95399.33160.169
3.004-3.2110.2181240.18419790.18621140.9380.94699.47970.185
3.211-3.4680.2171230.18918470.19119770.9490.95499.64590.191
3.468-3.7990.201820.18417350.18518220.9470.95999.72560.187
3.799-4.2470.167710.15715660.15716440.9620.96799.57420.161
4.247-4.9030.161810.13113710.13314540.9710.97799.86240.14
4.903-6.0030.154690.15911850.15812580.9770.97799.6820.165
6.003-8.480.203320.1949430.1949750.9570.9591000.199
8.48-128.190.185230.2095470.2085750.9620.95599.13040.212

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