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- PDB-8y2k: The crystal structure of QX006N-Fab -

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Basic information

Entry
Database: PDB / ID: 8y2k
TitleThe crystal structure of QX006N-Fab
Components
  • QX006N-Fab-HC
  • QX006N-Fab-LC
KeywordsIMMUNE SYSTEM / therapeutic monoclonal antibody / QX006N
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsLi, W. / Feng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071191 China
National Natural Science Foundation of China (NSFC)31971160 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural basis for the recognition of IFNAR1 by the humanized therapeutic monoclonal antibody QX006N for the treatment of systemic lupus erythematosus.
Authors: Chen, X. / Ke, H. / Li, W. / Yin, L. / Chen, W. / Chen, T. / Wu, Y. / Qiu, J. / Feng, W.
History
DepositionJan 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QX006N-Fab-LC
B: QX006N-Fab-HC
C: QX006N-Fab-LC
D: QX006N-Fab-HC


Theoretical massNumber of molelcules
Total (without water)95,4364
Polymers95,4364
Non-polymers00
Water00
1
A: QX006N-Fab-LC
B: QX006N-Fab-HC


Theoretical massNumber of molelcules
Total (without water)47,7182
Polymers47,7182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-29 kcal/mol
Surface area19750 Å2
MethodPISA
2
C: QX006N-Fab-LC
D: QX006N-Fab-HC


Theoretical massNumber of molelcules
Total (without water)47,7182
Polymers47,7182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-27 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.748, 137.496, 73.723
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody QX006N-Fab-LC


Mass: 23200.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody QX006N-Fab-HC


Mass: 24517.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 289 K / Method: evaporation, recrystallization
Details: 0.2 M potassium sodium tartrate tetrahydrate pH 4.5, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 21423 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.7 Å2 / CC1/2: 1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.85→2.95 Å / Num. unique obs: 2170 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→47.63 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 1005 4.71 %
Rwork0.215 --
obs0.2174 21335 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 0 0 6558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046695
X-RAY DIFFRACTIONf_angle_d0.7079099
X-RAY DIFFRACTIONf_dihedral_angle_d19.2172382
X-RAY DIFFRACTIONf_chiral_restr0.0461038
X-RAY DIFFRACTIONf_plane_restr0.0051159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.020.42041330.32242861X-RAY DIFFRACTION96
3.02-3.210.29691670.27352855X-RAY DIFFRACTION98
3.21-3.460.28721430.25712917X-RAY DIFFRACTION100
3.46-3.810.30341340.23632930X-RAY DIFFRACTION99
3.81-4.360.29011520.20372903X-RAY DIFFRACTION98
4.36-5.490.22011370.17712914X-RAY DIFFRACTION99
5.49-47.630.22091390.18722950X-RAY DIFFRACTION98

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