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- PDB-1a8j: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG) COMPLEX WITH ASPARTAME -

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Basic information

Entry
Database: PDB / ID: 1a8j
TitleIMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG) COMPLEX WITH ASPARTAME
ComponentsIMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG)
KeywordsIMMUNOGLOBULIN / ASPARTAME / LIGAND BINDING / IMMUNOTHERAPEUTIC AGENT / SURROGATE RECEPTOR / MCG(HUMAN) BENCE-JONES DIMER
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular region / plasma membrane
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER / Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE MAP / Resolution: 2.7 Å
AuthorsEdmundson, A.B. / Manion, C.V.
Citation
Journal: Clin.Pharmacol.Ther. / Year: 1998
Title: Treatment of osteoarthritis with aspartame.
Authors: Edmundson, A.B. / Manion, C.V.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Three-Dimensional Structure of a Light Chain Dimer Crystallized in Water. Conformational Flexibility of a Molecule in Two Crystal Forms
Authors: Ely, K.R. / Herron, J.N. / Harker, M. / Edmundson, A.B.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG)
H: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2554
Polymers45,6662
Non-polymers5892
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-30 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.300, 72.300, 185.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG)


Mass: 22833.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FOUND IN THE URINE OF PATIENT MCG WITH A MULTIPLE MYELOMA AND AMYLOIDOSIS
Source: (natural) Homo sapiens (human) / References: UniProt: P01709
#2: Chemical ChemComp-PME / N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER / ASPARTAME


Mass: 294.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O5
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: 3.07 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.2
Details: PROTEIN WAS CRYSTALLIZED IN FRESH 1.9M AMMONIUM SULFATE BUFFERED AT PH 6.2 WITH PHOSPHATE AND THE MOTHER LIQUOR WAS SATURATED WITH ASPARTAME.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.9 Mammonium sulfate11
2phosphate11
3aspartame11

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: DIFFRACTOMETER / Date: Nov 1, 1988
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 10570 / % possible obs: 62 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 17 Å2 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.82 Å / Mean I/σ(I) obs: 7 / % possible all: 30

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: DIFFERENCE MAP / Resolution: 2.7→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.38 988 10 %RANDOM
Rwork0.22 ---
obs0.22 9627 62 %-
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 58 0 3254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
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
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 54 10 %
Rwork0.29 512 -
obs--30 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg31.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65

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