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- PDB-2rgs: FC-fragment of monoclonal antibody IGG2B from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 2rgs
TitleFC-fragment of monoclonal antibody IGG2B from Mus musculus
ComponentsIg gamma-2B heavy chain
KeywordsIMMUNE SYSTEM / Fc-fragment / immunoglobulin / glycosylation
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsKolenko, P. / Duskova, J. / Skalova, T. / Dohnalek, J. / Hasek, J.
CitationJournal: Immunology / Year: 2008
Title: New insights into intra- and intermolecular interactions of immunoglobulins: crystal structure of mouse IgG2b-Fc at 2.1-A resolution
Authors: Kolenko, P. / Dohnalek, J. / Duskova, J. / Skalova, T. / Collard, R. / Hasek, J.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Ig gamma-2B heavy chain
B: Ig gamma-2B heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3134
Polymers49,0622
Non-polymers3,2512
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint59 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.946, 63.956, 72.624
Angle α, β, γ (deg.)90.00, 103.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Ig gamma-2B heavy chain / Ig gamma-2B chain C region / membrane-bound form / Ig gamma-2B chain C


Mass: 24530.783 Da / Num. of mol.: 2 / Fragment: Fc-fragment / Source method: isolated from a natural source / Details: specific for carbonic anhydrase / Source: (natural) Mus musculus (house mouse) / Cell line: MYELOMA NS-0 AND MICE SPLEEN CELLS HYBRIDOME / Strain: BALB/C / References: UniProt: P01867
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-2-1-2-1-3-4/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG2000, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 34014 / Num. obs: 34014 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.91 / Num. unique all: 2820 / Rsym value: 0.449 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FC-FRAGMENT OF PDB ENTRY 1IGT

1igt


Resolution: 2.13→20 Å / Cor.coef. Fo:Fc: 0.936 / SU B: 3.445 / SU ML: 0.094 / Isotropic thermal model: Isotropic / Cross valid method: thoughout / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / Stereochemistry target values: REFMAC5 Dictionaries
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT INCLUDED IN REFINEMENT OUTPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1670 -RANDOM
Rwork0.2006 ---
all0.20148 34014 --
obs0.20148 34014 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.871 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20.26 Å2
2---0.27 Å20 Å2
3----1.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 220 533 4046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223700
X-RAY DIFFRACTIONr_angle_refined_deg1.5552.0285070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.87725.226155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94315624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5941513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022603
X-RAY DIFFRACTIONr_nbd_refined0.2010.21606
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2457
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.211
X-RAY DIFFRACTIONr_mcbond_it0.921.52170
X-RAY DIFFRACTIONr_mcangle_it1.51123482
X-RAY DIFFRACTIONr_scbond_it2.06331714
X-RAY DIFFRACTIONr_scangle_it3.1684.51587

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