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- PDB-3mcg: THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED I... -

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Entry
Database: PDB / ID: 3mcg
TitleTHREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS
ComponentsIMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / 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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 space / 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 / 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
: / Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEly, K.R. / Herron, J.N. / Edmundson, A.B.
Citation
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.
#1: Journal: Mol.Immunol. / Year: 1987
Title: The Binding of Opioid Peptides to the Mcg Light Chain Dimer. Flexible Keys and Adjustable Locks
Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D.
#2: Journal: Progress in Immunology V / Year: 1983
Title: Three-Dimensional Structure of the Orthorhombic Form of the Mcg Bence-Jones Dimer
Authors: Ely, K.R. / Herron, J.N. / Edmundson, A.B.
#3: Journal: Biochemistry / Year: 1982
Title: Small-Angle Neutron Scattering Study of Bence-Jones Protein Mcg. Comparison of Structures in Solution and in Crystal
Authors: Schiffer, M. / Stevens, F.J. / Westholm, F.A. / Kim, S.S. / Carlson, R.D.
#4: Journal: Biochemistry / Year: 1980
Title: Marked Structural Differences of the Mcg Bence-Jones Dimer in Two Crystal Systems
Authors: Abola, E.E. / Ely, K.R. / Edmundson, A.B.
#5: Journal: Biochemistry / Year: 1978
Title: Crystal Properties as Indicators of Conformational Changes During Ligand Binding or Interconversion of Mcg Light Chain Isomers
Authors: Ely, K.R. / Firca, J.R. / Williams, K.J. / Abola, E.E. / Fenton, J.M. / Schiffer, M. / Panagiotopoulos, N.C. / Edmundson, A.B.
#6: Journal: Biochemistry / Year: 1978
Title: Interconversion of Conformational Isomers of Light Chains in the Mcg Immunoglobulins
Authors: Firca, J.R. / Ely, K.R. / Kremser, P. / Westholm, F.A. / Dorrington, K.J. / Edmundson, A.B.
#7: Journal: Sci.Am. / Year: 1977
Title: The Antibody Combining Site
Authors: Capra, J.D. / Edmundson, A.B.
#8: Journal: Antibodies in Human Diagnosis and Therapy / Year: 1977
Title: Implications of Conformational Isomerism and Rotational Allomerism to the Binding of Small Molecules by the Mcg Bence-Jones Dimer
Authors: Edmundson, A.B. / Abola, E.E. / Ely, K.R. / Firca, J.R. / Panagiotopoulos, N.C. / Schiffer, M. / Westholm, F.A.
#9: Journal: FED.PROC. / Year: 1976
Title: Conformational Isomerism,Rotational Allomerism, and Divergent Evolution in Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E. / Schiffer, M. / Panagiotopoulos, N. / Deutsch, H.F.
#10: Journal: Biochemistry / Year: 1975
Title: Rotational Allomerism and Divergent Evolution of Domains in Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E. / Schiffer, M. / Panagiotopoulos, N.
#11: Journal: Biochemistry / Year: 1974
Title: Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambda-Type Bence-Jones Dimer
Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A. / Fausch, M.D. / Deutsch, H.F.
#12: Journal: Progress in Immunology II / Year: 1974
Title: Structure and Binding Properties of a Lambda-Type Bence-Jones Dimer
Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A.
#13: Journal: Biochemistry / Year: 1974
Title: Primary Structure of the Mcg Lambda Chain
Authors: Fett, J.W. / Deutsch, H.F.
#14: Journal: Biochemistry / Year: 1973
Title: Preparation and Properties of a Bence-Jones Dimer with Mercury Inserted Into the Interchain Disulfide Bond
Authors: Ely, K.R. / Girling, R.L. / Schiffer, M. / Cunningham, D.E. / Edmundson, A.B.
#15: Journal: Biochemistry / Year: 1973
Title: Structure of a Lambda-Type Bence-Jones Protein at 3.5-Angstroms Resolution
Authors: Schiffer, M. / Girling, R.L. / Ely, K.R. / Edmundson, A.B.
#16: Journal: Prog.Mol.Subcell.Biol. / Year: 1973
Title: Structural Features of Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Schiffer, M. / Ely, K.R. / Wood, M.K.
#17: Journal: Biochemistry / Year: 1972
Title: Structure of a Lambda-Type Bence-Jones Protein at 6-Angstroms Resolution
Authors: Edmundson, A.B. / Schiffer, M. / Ely, K.R. / Wood, M.K.
#18: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Crystallographic Studies of an Igg Immunoglobulin and the Bence-Jones Protein from One Patient
Authors: Edmundson, A.B. / Schiffer, M. / Wood, M.K. / Hardman, K.D. / Ely, K.R. / Ainsworth, C.F.
History
DepositionMay 9, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
2: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,6662
Polymers45,6662
Non-polymers00
Water4,792266
1
1: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
2: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)

1: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
2: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)91,3324
Polymers91,3324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 81.900, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22833.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: PIR: S14675, UniProt: P01709*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: microdialysis
Details: taken from Abola, E.E. et al (1980). Biochemistry, 19, 432-439.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135-40 mg/mlprotein11
20.02 MTris-HCl12in 0.001 M in EDTA

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 7273 / Observed criterion σ(I): 3

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→7 Å / σ(I): 3 /
RfactorNum. reflection
obs0.208 7273
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 0 266 3478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.03
X-RAY DIFFRACTIONp_angle_d0.0560.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.03
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_restr0.0140.025
X-RAY DIFFRACTIONp_chiral_restr0.3410.15
X-RAY DIFFRACTIONp_singtor_nbd0.2880.5
X-RAY DIFFRACTIONp_multtor_nbd0.4340.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3150.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.73
X-RAY DIFFRACTIONp_staggered_tor26.715
X-RAY DIFFRACTIONp_orthonormal_tor3320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 3 / Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. reflection obs: 7273 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 7.85 Å2

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