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- PDB-2fbj: REFINED CRYSTAL STRUCTURE OF THE GALACTAN-BINDING IMMUNOGLOBULIN ... -

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Basic information

Entry
Database: PDB / ID: 2fbj
TitleREFINED CRYSTAL STRUCTURE OF THE GALACTAN-BINDING IMMUNOGLOBULIN FAB J539 AT 1.95-ANGSTROMS RESOLUTION
Components(IGA-KAPPA J539 FAB ...) x 2
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin production / positive regulation of B cell activation / phagocytosis, recognition / immunoglobulin complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway ...immunoglobulin production / positive regulation of B cell activation / phagocytosis, recognition / immunoglobulin complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / adaptive immune response / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig kappa chain V-VI region J539 / Ig heavy chain V region J539
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsBhat, T.N. / Padlan, E.A. / Davies, D.R.
Citation
Journal: To be Published
Title: Refined Crystal Structure of the Galactan-Binding Immunoglobulin Fab J539 at 1.95-Angstroms Resolution
Authors: Bhat, T.N. / Padlan, E.A. / Davies, D.R.
#1: Journal: Proteins / Year: 1986
Title: The Galactan-Binding Immunoglobulin Fab J539. An X-Ray Diffraction Study at 2.6-Angstroms Resolution
Authors: Suh, S.W. / Bhat, T.N. / Navia, M.A. / Cohen, G.H. / Rao, D.N. / Rudikoff, S. / Davies, D.R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: Crystal Structure of Galactan-Binding Mouse Immunoglobulin J539 Fab at 4.5-Angstroms Resolution
Authors: Navia, M.A. / Segal, D.M. / Padlan, E.A. / Davies, D.R. / Rao, N. / Rudikoff, S. / Potter, M.
History
DepositionAug 18, 1989Processing site: BNL
SupersessionJul 15, 1990ID: 1FBJ
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 11, 2013Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGA-KAPPA J539 FAB (LIGHT CHAIN)
H: IGA-KAPPA J539 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2925
Polymers47,2322
Non-polymers1,0603
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-27 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.018, 74.289, 131.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE DISACCHARIDE, WHOSE FORMULA IS - NAG(1) - NAG(2) IS LINKED TO ASN H 59 THE TRISACCHARIDE, WHOSE FORMULA IS - NAG(3) - NAG(5) | FUC(4) IS LINKED TO ASN H 156
2: RESIDUES PRO L 8, PRO L 93, PRO L 140, PRO H 139 AND PRO H ARE CIS-PROLINES.

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody IGA-KAPPA J539 FAB (LIGHT CHAIN)


Mass: 23282.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 437099, UniProt: P01679*PLUS
#2: Antibody IGA-KAPPA J539 FAB (HEAVY CHAIN)


Mass: 23948.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01810

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 376 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.95 Å / σ(F): 2.5 /
RfactorNum. reflection
obs0.194 28312
Refinement stepCycle: LAST / Highest resolution: 1.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 67 375 3761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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