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- PDB-3g6a: Crystal structure of anti-IL-13 antibody CNTO607 -

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Basic information

Entry
Database: PDB / ID: 3g6a
TitleCrystal structure of anti-IL-13 antibody CNTO607
Components
  • CNTO607 Fab Heavy chain
  • CNTO607 Fab Light chain
KeywordsIMMUNE SYSTEM / IL-13 / antibody / Fab / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Epitope mapping of anti-interleukin-13 neutralizing antibody CNTO607.
Authors: Teplyakov, A. / Obmolova, G. / Wu, S.J. / Luo, J. / Kang, J. / O'Neil, K. / Gilliland, G.L.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CNTO607 Fab Light chain
H: CNTO607 Fab Heavy chain
A: CNTO607 Fab Light chain
B: CNTO607 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)94,1624
Polymers94,1624
Non-polymers00
Water4,864270
1
L: CNTO607 Fab Light chain
H: CNTO607 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0812
Polymers47,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21.6 kcal/mol
Surface area19970 Å2
MethodPISA
2
A: CNTO607 Fab Light chain
B: CNTO607 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0812
Polymers47,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-21.6 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.050, 108.050, 78.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Antibody CNTO607 Fab Light chain


Mass: 22619.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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 CNTO607 Fab Heavy chain


Mass: 24461.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Human Embryonic Kidney 293 cells / Cell line (production host): HEK 293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFAB WAS OBTAINED BY PAPAIN CLEAVAGE OF ANTIBODY.

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4
Details: 0.1 M CAPS pH 10.4, 18% PEG 3350, 3% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 12, 2006 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 52686 / Num. obs: 52686 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 49.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.437 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.222 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2674 5.1 %RANDOM
Rwork0.208 ---
all0.212 49847 --
obs0.212 49847 94.7 %-
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: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.222 Å0.241 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 0 270 6738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9479080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3955860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90624.803254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36215988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3161520
X-RAY DIFFRACTIONr_chiral_restr0.1290.21020
X-RAY DIFFRACTIONr_gen_planes_refined00.025064
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.22754
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.24428
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.87124397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.55146944
X-RAY DIFFRACTIONr_scbond_it13.52682630
X-RAY DIFFRACTIONr_scangle_it15.05682136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 198 -
Rwork0.238 3636 -
obs--99.9 %

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