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- PDB-3kyk: Crystal structure of li33 Igg1 Fab -

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Basic information

Entry
Database: PDB / ID: 3kyk
TitleCrystal structure of li33 Igg1 Fab
Components
  • Heavy Chain Li33 IgG1
  • Light Chain Li33 IgG1
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy Chain Li33 IgG1
L: Light Chain Li33 IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1106
Polymers47,7262
Non-polymers3844
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-80 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.632, 90.632, 215.041
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody Heavy Chain Li33 IgG1


Mass: 24304.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Heavy chain Li33 / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light Chain Li33 IgG1


Mass: 23421.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Light chain Li33 / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2M ammonium sulfate, 0.1M sodium acetate pH 3.5 and 0.1M TCEP, 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: 0.97961 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 9320 / Num. obs: 9258 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.8 % / Rmerge(I) obs: 0.221 / Χ2: 0.773 / Net I/σ(I): 3.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.571 / Num. unique all: 888 / Χ2: 0.736 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å38.21 Å
Translation4 Å38.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B2X

2b2x


Resolution: 3.2→44.34 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.812 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.777 / SU B: 13.1 / SU ML: 0.236 / SU Rfree: 0.577 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29 442 4.8 %RANDOM
Rwork0.194 ---
obs0.198 9257 99.91 %-
all-9331 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.88 Å2 / Biso mean: 18.413 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 20 38 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223349
X-RAY DIFFRACTIONr_angle_refined_deg2.3811.9584562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.95429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14624.122131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.62715512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0451514
X-RAY DIFFRACTIONr_chiral_restr0.1350.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212518
X-RAY DIFFRACTIONr_mcbond_it0.7411.52133
X-RAY DIFFRACTIONr_mcangle_it1.45123433
X-RAY DIFFRACTIONr_scbond_it2.10931216
X-RAY DIFFRACTIONr_scangle_it3.5554.51129
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 31 -
Rwork0.213 621 -
all-652 -
obs--99.54 %

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