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- PDB-1dcl: MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRY... -

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Basic information

Entry
Database: PDB / ID: 1dcl
TitleMCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRYSTALLIZED FROM AMMONIUM SULFATE
ComponentsMCG
KeywordsIMMUNOGLOBULIN / BENCE JONES / ANTIBODY / MULTIPLE QUATERNARY STRUCTURES
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 / Potential therapeutics for SARS / adaptive immune response / 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
Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSchiffer, M. / Xu, Z.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: Am.Cryst.Assoc.,Abstr.Papers (Annual Meeting) / Year: 1988
Title: The Refinement and Structure of Mcg Bence-Jones Dimer at 2.3 Angstroms Resolution
Authors: Xu, Z.B. / Schiffer, M.
#2: Journal: Biochemistry / Year: 1973
Title: Structure of a Lambda-Type Bence-Jones Protein at 3.5-A Resolution
Authors: Schiffer, M. / Girling, R.L. / Ely, K.R. / Edmundson, A.B.
History
DepositionOct 16, 1995Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 30, 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
A: MCG
B: MCG


Theoretical massNumber of molelcules
Total (without water)45,6362
Polymers45,6362
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-25 kcal/mol
Surface area19010 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 MCG / BENCE-JONES PROTEIN


Mass: 22818.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: A LAMBDA V TYPE LIGHT-CHAIN DIMER / Source: (natural) Homo sapiens (human) / References: UniProt: P01709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growDetails: CRYSTALLIZED FROM AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / Details: Abola, E.E., (1980) Biochemistry, 19, 432.
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.14 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 413 3621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d2.6
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.14 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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