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- PDB-3i2c: Crystal structure of anti-IL-23 antibody CNTO4088 -

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Basic information

Entry
Database: PDB / ID: 3i2c
TitleCrystal structure of anti-IL-23 antibody CNTO4088
Components
  • CNTO4088 HEAVY CHAIN
  • CNTO4088 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IL-23 / antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Noncanonical conformation of CDR L1 in the anti-IL-23 antibody CNTO4088.
Authors: Teplyakov, A. / Obmolova, G. / Rogers, A. / Gilliland, G.L.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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
L: CNTO4088 LIGHT CHAIN
H: CNTO4088 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9513
Polymers47,8582
Non-polymers921
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-30 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.430, 99.430, 115.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Antibody CNTO4088 LIGHT CHAIN


Mass: 23842.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Human Embryonic Kidney 293 cells / Cell line (production host): HEK 293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#2: Antibody CNTO4088 HEAVY CHAIN


Mass: 24016.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Human Embryonic Kidney 293 cells / Cell line (production host): HEK 293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M CITRATE PH 3.5, 24% PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 3, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 13889 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.169
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.549 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EO8

1eo8


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.191 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23503 684 5 %RANDOM
Rwork0.19594 ---
obs0.19783 13044 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refine analyzeLuzzati coordinate error free: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 6 2 3359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9494694
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11624135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01315536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6791514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2525
X-RAY DIFFRACTIONr_gen_planes_refined00.022604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21345
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71722231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.31143546
X-RAY DIFFRACTIONr_scbond_it6.75781387
X-RAY DIFFRACTIONr_scangle_it8.25181148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 54 -
Rwork0.303 945 -
obs--100 %

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