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- PDB-1plg: EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOP... -

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Basic information

Entry
Database: PDB / ID: 1plg
TitleEVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID
Components(IGG2A=KAPPA=) x 2
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / If kappa light chain / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsEvans, S.V. / Sigurskjold, B.W. / Jennings, H.J. / Brisson, J.-R. / Tse, W.C. / To, R. / Altman, E. / Frosch, M. / Weisgerber, C. / Kratzin, H. ...Evans, S.V. / Sigurskjold, B.W. / Jennings, H.J. / Brisson, J.-R. / Tse, W.C. / To, R. / Altman, E. / Frosch, M. / Weisgerber, C. / Kratzin, H. / Klebert, S. / Vaesen, M. / Bitter-Suermann, D. / Rose, D.R. / Young, N.M. / Bundle, D.R.
Citation
Journal: Biochemistry / Year: 1995
Title: Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid.
Authors: Evans, S.V. / Sigurskjold, B.W. / Jennings, H.J. / Brisson, J.R. / To, R. / Tse, W.C. / Altman, E. / Frosch, M. / Weisgerber, C. / Kratzin, H.D. / Klebert, S. / Vaesen, M. / Bitter-Suermann, ...Authors: Evans, S.V. / Sigurskjold, B.W. / Jennings, H.J. / Brisson, J.R. / To, R. / Tse, W.C. / Altman, E. / Frosch, M. / Weisgerber, C. / Kratzin, H.D. / Klebert, S. / Vaesen, M. / Bitter-Suermann, D. / Rose, D.R. / Young, N.M. / Bundle, D.R.
#1: Journal: Biochemistry / Year: 1992
Title: Helical Epitope of the Group B Meningococcal Alpha(2->8)-Linked Sialic Acid Polysaccharide
Authors: Brisson, J.-R. / Baumann, H. / Imberty, A. / Perez, S. / Jennings, H.J.
History
DepositionApr 24, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Jun 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG2A=KAPPA=
H: IGG2A=KAPPA=


Theoretical massNumber of molelcules
Total (without water)46,7602
Polymers46,7602
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-27 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.140, 91.210, 141.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO L 8
2: LYS L 44 - PRO L 45 OMEGA = 212.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO L 100 / 4: CIS PROLINE - PRO L 146 / 5: CIS PROLINE - PRO H 151 / 6: CIS PROLINE - PRO H 153 / 7: CIS PROLINE - PRO H 193

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Components

#1: Antibody IGG2A=KAPPA=


Mass: 23737.297 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT THAT BINDS POLYSIALIC ACID / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: PIR: S16112, UniProt: A2NHM3*PLUS
#2: Antibody IGG2A=KAPPA=


Mass: 23022.732 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT THAT BINDS POLYSIALIC ACID / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.7 mg/mlFab1drop
316-18 %PEG40001reservoir
40.1 MHEPES1reservoir
50.1 Mammonium sulfate1reservoir
60.01 M1reservoirNaN3
2reservoir solution1drop0.006 ml

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Apr 24, 1991
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 8.5 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. all: 10611 / Num. obs: 10590 / % possible obs: 99.8 % / Num. measured all: 87625

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / σ(I): 3 /
RfactorNum. reflection
Rwork0.164 -
obs0.164 11503
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 34 3325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_d0.040.052
X-RAY DIFFRACTIONx_planar_d0.060.065
X-RAY DIFFRACTIONx_plane_restr0.0250.03
X-RAY DIFFRACTIONx_chiral_restr0.1250.125

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