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- PDB-1lil: BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER -

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Basic information

Entry
Database: PDB / ID: 1lil
TitleBENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER
ComponentsLAMBDA III BENCE JONES PROTEIN CLE
KeywordsIMMUNOGLOBULIN / BENCE JONES PROTEIN
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / 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 / B cell receptor signaling pathway / 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 / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda constant 1 / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchiffer, M. / Huang, D.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer.
Authors: Huang, D.B. / Ainsworth, C. / Solomon, A. / Schiffer, M.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Preliminary Crystallographic Data on the Human Lambda III Bence Jones Protein Dimer Cle
Authors: Stevens, F.J. / Westholm, F.A. / Panagiotopoulos, N. / Solomon, A. / Schiffer, M.
History
DepositionMay 13, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: 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 ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / refine / 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 / _refine.pdbx_starting_model / _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: LAMBDA III BENCE JONES PROTEIN CLE
B: LAMBDA III BENCE JONES PROTEIN CLE


Theoretical massNumber of molelcules
Total (without water)45,3842
Polymers45,3842
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.170, 72.540, 49.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody LAMBDA III BENCE JONES PROTEIN CLE


Mass: 22692.049 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01842, UniProt: P0DOY3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growpH: 7 / Details: 1.8 M AMMONIUM SULFATE PH 7.0
Crystal grow
*PLUS
Method: microdialysis / Details: Stevens, F.J., (1981) J.Mol.Biol., 147, 179.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
23.0 Mammonium sulfate12
31.8 Mammonium hydroxide12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.65 Å / Num. obs: 11373 / % possible obs: 92 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.047
Reflection
*PLUS
Lowest resolution: 10.5 Å / Num. measured all: 55038

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Processing

Software
NameVersionClassification
LARRYWISEMAN'S FOURIER-BESSELdata collection
SCALINGdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
LARRYWISEMAN'S FOURIER-BESSELdata reduction
SCALINGdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→10 Å / σ(F): 2 / Details: X-PLOR WAS USED IN THE EARLY STAGES OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.34 -5 %RANDOM
Rwork0.19 ---
obs0.2 8684 71 %-
Displacement parametersBiso mean: 15.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 0 123 3313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
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_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1690.15
X-RAY DIFFRACTIONp_singtor_nbd0.210.5
X-RAY DIFFRACTIONp_multtor_nbd0.310.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.280.5
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor24.613
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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