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- PDB-6tkb: ChiLob 7/4 H2 HC-C224S F(ab')2 -

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Basic information

Entry
Database: PDB / ID: 6tkb
TitleChiLob 7/4 H2 HC-C224S F(ab')2
Components
  • Chilob 7/4 H2 heavy chain C224S
  • Chilob 7/4 H2 kappa chain
KeywordsIMMUNE SYSTEM / immunology / antibody / igg / igg2
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 20, 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
III: Chilob 7/4 H2 heavy chain C224S
MMM: Chilob 7/4 H2 kappa chain


Theoretical massNumber of molelcules
Total (without water)97,1264
Polymers97,1264
Non-polymers00
Water8,233457
1
HHH: Chilob 7/4 H2 heavy chain C224S
LLL: Chilob 7/4 H2 kappa chain


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-29 kcal/mol
Surface area19760 Å2
MethodPISA
2
III: Chilob 7/4 H2 heavy chain C224S
MMM: Chilob 7/4 H2 kappa chain


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-26 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.758, 95.191, 150.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Chilob 7/4 H2 heavy chain C224S


Mass: 25099.102 Da / Num. of mol.: 2
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.: 2
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.: 457 / 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: 2.78 Å3/Da / Density % sol: 55.75 % / Description: irregular rod with central needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 8000, cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2→47.641 Å / Num. obs: 76835 / % possible obs: 99.1 % / Redundancy: 29.5 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Net I/σ(I): 25.3
Reflection shellResolution: 2→2.04 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4462 / CC1/2: 0.775 / Rpim(I) all: 0.342

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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→47.641 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2291 3619 4.952 %
Rwork0.1823 --
all0.185 --
obs-73078 99.701 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.678 Å2
Baniso -1Baniso -2Baniso -3
1--1.185 Å20 Å20 Å2
2--1.477 Å20 Å2
3----0.292 Å2
Refinement stepCycle: LAST / Resolution: 2→47.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 0 457 7160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136867
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176055
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.6479345
X-RAY DIFFRACTIONr_angle_other_deg2.4341.57114183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3385873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48323.776294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.818151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1451521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027669
X-RAY DIFFRACTIONr_gen_planes_other0.010.021354
X-RAY DIFFRACTIONr_nbd_refined0.1880.21064
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.25544
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23302
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2457
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.25
X-RAY DIFFRACTIONr_nbd_other0.1860.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.221
X-RAY DIFFRACTIONr_mcbond_it3.7184.3913504
X-RAY DIFFRACTIONr_mcbond_other3.7184.393503
X-RAY DIFFRACTIONr_mcangle_it5.0426.5634373
X-RAY DIFFRACTIONr_mcangle_other5.0416.5654374
X-RAY DIFFRACTIONr_scbond_it4.4254.8153363
X-RAY DIFFRACTIONr_scbond_other4.4114.8143362
X-RAY DIFFRACTIONr_scangle_it6.4937.0314972
X-RAY DIFFRACTIONr_scangle_other6.4937.0314972
X-RAY DIFFRACTIONr_lrange_it8.33551.0227401
X-RAY DIFFRACTIONr_lrange_other8.3250.8867316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3012500.2495085X-RAY DIFFRACTION99.7942
2.052-2.1080.2792750.2334937X-RAY DIFFRACTION99.7321
2.108-2.1690.292890.2264735X-RAY DIFFRACTION99.2297
2.169-2.2360.2692340.2114706X-RAY DIFFRACTION99.9393
2.236-2.3090.2721990.2024577X-RAY DIFFRACTION99.8536
2.309-2.390.2552250.1894402X-RAY DIFFRACTION99.5482
2.39-2.480.2532370.1924216X-RAY DIFFRACTION99.6197
2.48-2.5820.2292150.1874127X-RAY DIFFRACTION99.885
2.582-2.6970.2241710.1833938X-RAY DIFFRACTION99.8057
2.697-2.8280.2692090.1953740X-RAY DIFFRACTION99.7222
2.828-2.9810.2681900.1973582X-RAY DIFFRACTION99.4201
2.981-3.1620.2471810.1923392X-RAY DIFFRACTION100
3.162-3.380.2591760.1993214X-RAY DIFFRACTION100
3.38-3.6510.2261570.1912984X-RAY DIFFRACTION99.7143
3.651-3.9990.2061160.1812786X-RAY DIFFRACTION99.5199
3.999-4.470.1811500.1482499X-RAY DIFFRACTION99.8869
4.47-5.1610.1871120.1392234X-RAY DIFFRACTION100
5.161-6.3190.216910.1641936X-RAY DIFFRACTION100
6.319-8.9290.236830.1661497X-RAY DIFFRACTION99.5589
8.929-47.6410.168590.166872X-RAY DIFFRACTION99.2537

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