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- PDB-1lve: STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGH... -

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Entry
Database: PDB / ID: 1lve
TitleSTRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN
ComponentsLEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE
KeywordsIMMUNOGLOBULIN / BENCE-JONES PROTEIN
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / 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 / immunoglobulin complex / Initial triggering of complement / 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 / blood microparticle / 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
Immunoglobulin kappa variable 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchiffer, M. / Huang, D.-B. / Chang, C.-H.
Citation
Journal: Mol.Immunol. / Year: 1997
Title: Variable domain structure of kappaIV human light chain Len: high homology to the murine light chain McPC603.
Authors: Huang, D.B. / Chang, C.H. / Ainsworth, C. / Johnson, G. / Solomon, A. / Stevens, F.J. / Schiffer, M.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1996
Title: Structure of the Variable Domain of Human Immunoglobulin Kappa-Iv Light Chain Len
Authors: Huang, D.-B. / Ainsworth, C. / Chang, C.-H. / Stevens, F.J. / Schiffer, M.
#2: Journal: Protein Sci. / Year: 1995
Title: Recombinant Immunoglobulin Variable Domains Generated from Synthetic Genes Provide a System for in Vitro Characterization of Light-Chain Amyloid Proteins
Authors: Stevens, P.W. / Raffen, R. / Hanson, D.K. / Deng, Y.L. / Berrios-Hammond, M. / Westholm, F.A. / Murphy, C. / Eulitz, M. / Wetzel, R. / Solomon, A. / Schiffer, M. / Stevens, F.J.
History
DepositionJul 17, 1996Processing site: BNL
SupersessionJan 21, 1998ID: 1LVD
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE


Theoretical massNumber of molelcules
Total (without water)13,4231
Polymers13,4231
Non-polymers00
Water2,216123
1
A: LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE

A: LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE


Theoretical massNumber of molelcules
Total (without water)26,8462
Polymers26,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)43.110, 83.530, 54.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

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Components

#1: Antibody LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE


Mass: 13422.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01625, UniProt: P06312*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.84 Å3/Da / Density % sol: 33 %
Crystal growpH: 7 / Details: 1.5 M AMMONIUM SULFATE, PH 7.0
Crystal grow
*PLUS
Method: batch
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein11
21.5 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: PICKER / Detector: DIFFRACTOMETER / Date: 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→23.4 Å / Num. obs: 7471 / % possible obs: 99 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WAT (MONOMER 2)

Resolution: 1.95→10 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -5 %RANDOM
Rwork0.15 ---
obs0.16 5053 67 %-
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 123 1013
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.91
X-RAY DIFFRACTIONp_mcangle_it1.511.5
X-RAY DIFFRACTIONp_scbond_it1.581.5
X-RAY DIFFRACTIONp_scangle_it2.512
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1870.15
X-RAY DIFFRACTIONp_singtor_nbd0.2170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2770.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2590.3
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor24.313
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.222 / Num. reflection obs: 793

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