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- PDB-6nov: A Fab derived from ixekizumab -

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Basic information

Entry
Database: PDB / ID: 6nov
TitleA Fab derived from ixekizumab
Components
  • Fab Heavy Chain
  • Fab Light Chain
KeywordsIMMUNE SYSTEM / IL17 / IL-17 / Ixekizumab / Fab / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsDurbin, J.D. / Clawson, D.K. / Lu, F. / Tian, Y. / Lu, J. / Schmitt, M. / Atwell, S.
Citation
Journal: Mabs / Year: 2019
Title: Development of tibulizumab, a tetravalent bispecific antibody targeting BAFF and IL-17A for the treatment of autoimmune disease.
Authors: Benschop, R.J. / Chow, C.K. / Tian, Y. / Nelson, J. / Barmettler, B. / Atwell, S. / Clawson, D. / Chai, Q. / Jones, B. / Fitchett, J. / Torgerson, S. / Ji, Y. / Bina, H. / Hu, N. / Ghanem, M. ...Authors: Benschop, R.J. / Chow, C.K. / Tian, Y. / Nelson, J. / Barmettler, B. / Atwell, S. / Clawson, D. / Chai, Q. / Jones, B. / Fitchett, J. / Torgerson, S. / Ji, Y. / Bina, H. / Hu, N. / Ghanem, M. / Manetta, J. / Wroblewski, V.J. / Lu, J. / Allan, B.W.
#1: Journal: Mol. Pharm. / Year: 2016
Title: Therapeutic Antibody Engineering To Improve Viscosity and Phase Separation Guided by Crystal Structure.
Authors: Chow, C.K. / Allan, B.W. / Chai, Q. / Atwell, S. / Lu, J.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy Chain
B: Fab Light Chain
C: Fab Heavy Chain
D: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3435
Polymers96,7964
Non-polymers5471
Water5,837324
1
A: Fab Heavy Chain
B: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9453
Polymers48,3982
Non-polymers5471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-24 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: Fab Heavy Chain
D: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,3982
Polymers48,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.404, 197.497, 44.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody Fab Heavy Chain


Mass: 24269.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab Light Chain


Mass: 24129.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.69 Å3/Da / Density % sol: 54.28 % / Description: 150um plate
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% PEG 5000 MME/100 mM MES (pH 6.5)/200 mM ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→41.688 Å / Num. obs: 66339 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 35.6 Å2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.146 / Rsym value: 0.127 / Net I/av σ(I): 3.7 / Net I/σ(I): 8.1 / Num. measured all: 467195
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.147.30.7930.85836780340.340.9210.7932.199.9
2.14-2.257.20.5791.25541776690.2490.6740.5792.799.7
2.25-2.377.20.4441.45229072940.1930.5210.4443.499.6
2.37-2.517.10.3232.34946669200.140.3780.3234.299.4
2.51-2.687.10.2362.94576764650.1040.2780.2365.599.3
2.68-2.970.1594.34242060600.0710.1880.1597.499.1
2.9-3.186.90.1125.83866755910.0490.1310.1129.998.5
3.18-3.556.90.1015.63496350810.0440.1150.10113.399.6
3.55-4.16.80.1065.13121545680.0440.1190.1061699.8
4.1-5.026.90.09362676338850.0390.1040.09319.499.9
5.02-7.170.058102150130720.0240.0650.05820100
7.1-41.6886.10.0415.11035917000.0190.0460.0418.194.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
SCALA3.3.16data scaling
Cootmodel building
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→19.87 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.842 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2822 4.85 %RANDOM
Rwork0.238 ---
obs0.24 58224 99.2 %-
Displacement parametersBiso max: 136.81 Å2 / Biso mean: 44.77 Å2 / Biso min: 14.19 Å2
Baniso -1Baniso -2Baniso -3
1-12.1763 Å20 Å20 Å2
2--14.7165 Å20 Å2
3----26.8928 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.14→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 30 324 6781
Biso mean--45.31 44.03 -
Num. residues----861
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2143SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1111HARMONIC5
X-RAY DIFFRACTIONt_it6657HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion887SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6657HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9084HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion18.38
LS refinement shellResolution: 2.14→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3779 52 4.46 %
Rwork0.2919 1113 -
all0.2953 1165 -
obs--100 %

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