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- PDB-1fcc: CRYSTAL STRUCTURE OF THE C2 FRAGMENT OF STREPTOCOCCAL PROTEIN G I... -

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Basic information

Entry
Database: PDB / ID: 1fcc
TitleCRYSTAL STRUCTURE OF THE C2 FRAGMENT OF STREPTOCOCCAL PROTEIN G IN COMPLEX WITH THE FC DOMAIN OF HUMAN IGG
Components
  • IGG1 MO61 FC
  • STREPTOCOCCAL PROTEIN G (C2 FRAGMENT)
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG binding / Classical antibody-mediated complement activation / immunoglobulin receptor binding / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG binding / Classical antibody-mediated complement activation / immunoglobulin receptor binding / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / B cell receptor signaling pathway / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / Interleukin-4 and Interleukin-13 signaling / blood microparticle / antibacterial humoral response / adaptive immune response / Initial triggering of complement / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / 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. ...Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / 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 / : / Ubiquitin-like (UB roll) / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsSauer-Eriksson, A.E. / Kleywegt, G.J. / Uhlen, M. / Jones, T.A.
CitationJournal: Structure / Year: 1995
Title: Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG.
Authors: Sauer-Eriksson, A.E. / Kleywegt, G.J. / Uhlen, M. / Jones, T.A.
History
DepositionJan 17, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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
A: IGG1 MO61 FC
C: STREPTOCOCCAL PROTEIN G (C2 FRAGMENT)
B: IGG1 MO61 FC
D: STREPTOCOCCAL PROTEIN G (C2 FRAGMENT)


Theoretical massNumber of molelcules
Total (without water)59,3554
Polymers59,3554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.600, 110.600, 160.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO A 374
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.700155, -0.700538, -0.138305), (-0.708564, 0.657833, 0.255398), (-0.087885, 0.276852, -0.956887)
Vector: 75.59965, 34.53081, -13.57867)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED IN THIS ENTRY WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES OF THE OTHER MONOMERS IN THE ASYMMETRIC UNIT NOT PRESENTED IN THIS ENTRY.

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Components

#1: Protein IGG1 MO61 FC


Mass: 23519.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HYBRIDOMA / Gene: N-TERMINAL FRAGMENT OF / Plasmid: PEB2ZHIS GENE: N-TERMINAL FRAGMENT OF / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#2: Protein STREPTOCOCCAL PROTEIN G (C2 FRAGMENT)


Mass: 6157.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Genus: Streptococcus / Cell line: HYBRIDOMA / Gene: N-TERMINAL FRAGMENT OF / Plasmid: PEB2ZHIS GENE: N-TERMINAL FRAGMENT OF / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
Compound detailsFIVE AMINO ACIDS DIFFER IN THEIR AMIDATION STATES AND TWO HAVE THE ALLOTYPIC MARKER: E119, M121.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.2 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409.
Components of the solutions
*PLUS
Conc.: 10 mg/ml / Common name: protein

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 12297 / % possible obs: 72 %
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 9999 Å / Num. measured all: 41581 / Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→8 Å
RfactorNum. reflection% reflection
Rfree0.357 --
Rwork0.289 --
obs0.289 12297 72 %
Displacement parametersBiso mean: 41.6 Å2
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 0 0 4180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.56
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.89
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 3.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.56
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.89

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