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- PDB-3iu4: anti NeuGcGM3 ganglioside chimeric antibody chP3 -

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Basic information

Entry
Database: PDB / ID: 3iu4
Titleanti NeuGcGM3 ganglioside chimeric antibody chP3
Components
  • chP3 Fab heavy chain
  • chP3 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / ganglioside / idiotype
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEriksson, A. / Okvist, M. / Talavera, A. / Krengel, U.
CitationJournal: Mol.Immunol. / Year: 2009
Title: Crystal structure of an anti-ganglioside antibody, and modelling of the functional mimicry of its NeuGc-GM3 antigen by an anti-idiotypic antibody.
Authors: Talavera, A. / Eriksson, A. / Okvist, M. / Lopez-Requena, A. / Fernandez-Marrero, Y. / Perez, R. / Moreno, E. / Krengel, U.
History
DepositionAug 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: chP3 Fab heavy chain
L: chP3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7197
Polymers51,2382
Non-polymers4805
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-78 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.450, 153.450, 111.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11H-255-

SO4

21L-302-

HOH

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Components

#1: Antibody chP3 Fab heavy chain


Mass: 27775.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -VH y VK: Mus musculus (BALB/c) -CH y CK: Homo sapiens
Source: (gene. exp.) Mus musculus, Homo sapiens / Strain: BALB/c / Plasmid: pAH4604 / Cell line (production host): NS0 / Production host: Mus musculus (house mouse) / Strain (production host): BALB/c
#2: Antibody chP3 Fab light chain


Mass: 23463.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -VH y VK: Mus musculus (BALB/c) -CH y CK: Homo sapiens
Source: (gene. exp.) Mus musculus, Homo sapiens / Strain: BALB/c / Plasmid: pAE4622 / Cell line (production host): NS0 / Production host: Mus musculus (house mouse) / Strain (production host): BALB/c
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / pH: 6.5
Details: Final data were collected on a crystal obtained from crystallization conditions containing 30% polyethylene glycol (PEG) 10K, 0.1 M cacodylate pH 6.5 and 0.2 M ammonium sulfate, which had ...Details: Final data were collected on a crystal obtained from crystallization conditions containing 30% polyethylene glycol (PEG) 10K, 0.1 M cacodylate pH 6.5 and 0.2 M ammonium sulfate, which had grown to a size of 0.2x0.1x0.1 mm3 over 7.5 months. 15% glycerol was used as a cryo-protectant, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934
DetectorType: ADSC Q210 / Detector: CCD / Date: Oct 8, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.75→55.7 Å / Num. obs: 63026 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.515 / % possible all: 14.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY PDB 1CEL

1cel


Resolution: 1.75→49.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.084 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3370 5.1 %RANDOM
Rwork0.194 ---
obs0.196 63024 99.4 %-
all-66399 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.098 Å / Luzzati sigma a obs: 0.103 Å
Refinement stepCycle: LAST / Resolution: 1.75→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 25 421 3789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223478
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.9564753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81424.242132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91915557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9921513
X-RAY DIFFRACTIONr_chiral_restr0.1910.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212634
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_it1.4871.52209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42523591
X-RAY DIFFRACTIONr_scbond_it3.5431269
X-RAY DIFFRACTIONr_scangle_it5.2554.51162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 249 -
Rwork0.261 4658 -
obs--99.86 %

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