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- PDB-1igc: IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G F... -

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Basic information

Entry
Database: PDB / ID: 1igc
TitleIGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS
Components
  • IGG1-KAPPA MOPC21 FAB (HEAVY CHAIN)
  • IGG1-KAPPA MOPC21 FAB (LIGHT CHAIN)
  • STREPTOCOCCAL PROTEIN G (DOMAIN III)
KeywordsCOMPLEX (ANTIBODY/BINDING PROTEIN) / PROTEIN G / STREPTOCOCCUS / COMPLEX (ANTIBODY-BINDING PROTEIN) COMPLEX
Function / homology
Function and homology information


IgG binding / immunoglobulin complex / adaptive immune response / immune response / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / : / LPXTG cell wall anchor motif ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / : / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ig kappa chain V-V region MOPC 21 / : / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptococcus sp. G148 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsDerrick, J.P. / Wigley, D.B.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab.
Authors: Derrick, J.P. / Wigley, D.B.
#1: Journal: Biochemistry / Year: 1994
Title: Two Crystal Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison with NMR
Authors: Gallagher, T. / Alexander, P. / Bryan, P. / Gilliland, G.L.
#2: Journal: Nature / Year: 1992
Title: Crystal Structure of a Streptococcal Protein G Domain Bound to an Fab Fragment
Authors: Derrick, J.P. / Wigley, D.B.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Analysis of the Complex between a Mouse Fab Fragment and a Single Igg-Binding Domain from Streptococcal Protein G
Authors: Derrick, J.P. / Davies, G.J. / Dauter, Z. / Wilson, K.S. / Wigley, D.B.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of the Solution Structures of Domains II and III of Protein G from Streptococcus by 1H Nuclear Magnetic Resonance
Authors: Lian, L.-Y. / Derrick, J.P. / Sutcliff, M.J. / Yang, J.C. / Roberts, G.C.K.
#5: Journal: Biochemistry / Year: 1992
Title: 1.67 Angstroms X-Ray Structure of the B2 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison to the NMR Structure of the B1 Domain
Authors: Achari, A. / Hale, S.P. / Howard, A.J. / Clore, G.M. / Gronenborn, A.M. / Hardman, K.D. / Whitlow, M.
#6: Journal: Science / Year: 1991
Title: A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G
Authors: Gronenborn, A.M. / Filpula, D.R. / Essig, N.Z. / Achari, A. / Whitlow, M. / Wingfield, P.T. / Clore, G.M.
History
DepositionAug 5, 1994Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA MOPC21 FAB (LIGHT CHAIN)
H: IGG1-KAPPA MOPC21 FAB (HEAVY CHAIN)
A: STREPTOCOCCAL PROTEIN G (DOMAIN III)


Theoretical massNumber of molelcules
Total (without water)54,0703
Polymers54,0703
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.500, 70.500, 120.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO H 103 / 4: CIS PROLINE - PRO H 154 / 5: CIS PROLINE - PRO H 156

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Components

#1: Antibody IGG1-KAPPA MOPC21 FAB (LIGHT CHAIN)


Mass: 23556.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 JM101 / References: UniProt: P01634
#2: Antibody IGG1-KAPPA MOPC21 FAB (HEAVY CHAIN)


Mass: 23856.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 JM101 / References: UniProt: P01783
#3: Protein STREPTOCOCCAL PROTEIN G (DOMAIN III)


Mass: 6657.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. G148 (bacteria) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 JM101 / References: UniProt: P06654
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE ARE NO RESIDUES MISSING FROM THE LIGHT CHAIN. THERE ARE NO RESIDUES MISSING FROM THE N ...THERE ARE NO RESIDUES MISSING FROM THE LIGHT CHAIN. THERE ARE NO RESIDUES MISSING FROM THE N TERMINUS OF THE HEAVY CHAIN. THE SITE OF PROTEOLYSIS AT THE C TERMINUS OF THE HEAVY CHAIN IS UNDEFINED, SO IT IS NOT KNOWN WHETHER THERE ARE ANY RESIDUES MISSING THERE. THE FIRST THREE RESIDUES ARE MISSING FROM THE N TERMINUS OF PROTEIN G DOMAIN III: MET A 1, THR A 2, AND PRO A 3.
Source detailsMOPC21 (IGG1 KAPPA) WAS ISOLATED FROM ASCITES FLUID, GENERATED BY A MINERAL OIL-INDUCED ...MOPC21 (IGG1 KAPPA) WAS ISOLATED FROM ASCITES FLUID, GENERATED BY A MINERAL OIL-INDUCED PLASMACYTOMA. THE PRODUCT WAS OBTAINED COMMERCIALLY (SIGMA PRODUCT NUMBER M7894). FAB FRAGMENT WAS GENERATED BY PROTEOLYSIS OF INTACT IGG1 AS DESCRIBED BY DERRICK ET AL., 1992 (REFERENCE 3 ABOVE). PROTEIN G: SEE LIAN ET AL. 1992 FOR DETAILS (REFERENCE 4 ABOVE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal grow
*PLUS
pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMsodium acetate1reservoir
30.01 %(w/v)sodium azide1reservoir
424-26 %(w/v)PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Wavelength: 1 Å
DetectorDate: Apr 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 17204 / % possible obs: 98.7 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.079

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→20 Å / Rfactor obs: 0.168
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 0 345 4117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0560.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.06
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_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1330.12
X-RAY DIFFRACTIONp_singtor_nbd0.2360.5
X-RAY DIFFRACTIONp_multtor_nbd0.3210.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2860.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.565
X-RAY DIFFRACTIONp_staggered_tor25.0415
X-RAY DIFFRACTIONp_orthonormal_tor27.0920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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