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- PDB-3kym: Crystal structure of Li33 IgG2 di-Fab -

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Basic information

Entry
Database: PDB / ID: 3kym
TitleCrystal structure of Li33 IgG2 di-Fab
Components
  • Heavy Chain Li33 IgG2
  • Light Chain Li33 IgG2
KeywordsIMMUNE SYSTEM / IgG2 monoclonal anti-Lingo
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsSilvian, L.F. / Pepinsky, R.B. / Walus, L.
CitationJournal: Protein Sci. / Year: 2010
Title: Improving the solubility of anti-LINGO-1 monoclonal antibody Li33 by isotype switching and targeted mutagenesis.
Authors: Pepinsky, R.B. / Silvian, L. / Berkowitz, S.A. / Farrington, G. / Lugovskoy, A. / Walus, L. / Eldredge, J. / Capili, A. / Mi, S. / Graff, C. / Garber, E.
History
DepositionDec 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Light Chain Li33 IgG2
B: Heavy Chain Li33 IgG2
C: Light Chain Li33 IgG2
D: Heavy Chain Li33 IgG2
E: Light Chain Li33 IgG2
F: Heavy Chain Li33 IgG2
G: Light Chain Li33 IgG2
H: Heavy Chain Li33 IgG2
I: Light Chain Li33 IgG2
J: Heavy Chain Li33 IgG2
K: Light Chain Li33 IgG2
L: Heavy Chain Li33 IgG2
M: Light Chain Li33 IgG2
N: Heavy Chain Li33 IgG2
O: Light Chain Li33 IgG2
P: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)383,29216
Polymers383,29216
Non-polymers00
Water0
1
A: Light Chain Li33 IgG2
B: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-30 kcal/mol
Surface area20250 Å2
MethodPISA
2
C: Light Chain Li33 IgG2
D: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-29 kcal/mol
Surface area20500 Å2
MethodPISA
3
E: Light Chain Li33 IgG2
F: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-29 kcal/mol
Surface area20350 Å2
MethodPISA
4
G: Light Chain Li33 IgG2
H: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-30 kcal/mol
Surface area20160 Å2
MethodPISA
5
I: Light Chain Li33 IgG2
J: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-31 kcal/mol
Surface area20560 Å2
MethodPISA
6
K: Light Chain Li33 IgG2
L: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-26 kcal/mol
Surface area20800 Å2
MethodPISA
7
M: Light Chain Li33 IgG2
N: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-27 kcal/mol
Surface area20590 Å2
MethodPISA
8
O: Light Chain Li33 IgG2
P: Heavy Chain Li33 IgG2


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-28 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.669, 109.545, 118.433
Angle α, β, γ (deg.)61.46, 79.29, 87.59
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Light Chain Li33 IgG2


Mass: 23421.965 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Heavy Chain Li33 IgG2


Mass: 24489.480 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12% PEG3350, 0.1M phosphate citrate pH 4, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9797 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. all: 124078 / Num. obs: 122107 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.8
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GIZ

3giz


Resolution: 2.62→19.96 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.831 / SU B: 20.606 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R: 1.758 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33904 5749 5 %RANDOM
Rwork0.25944 ---
obs0.26686 109595 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.02 Å20.01 Å2
2---0.01 Å2-0.02 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.62→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26358 0 0 0 26358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02227026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.94936782
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98153432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85223.9291097
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.564154265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.77115134
X-RAY DIFFRACTIONr_chiral_restr0.1130.24081
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.517132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.167227658
X-RAY DIFFRACTIONr_scbond_it1.30639894
X-RAY DIFFRACTIONr_scangle_it2.2544.59124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 361 -
Rwork0.558 7066 -
obs--85.53 %

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