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- PDB-1wtl: COMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRU... -

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Basic information

Entry
Database: PDB / ID: 1wtl
TitleCOMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRUCTURAL ORIGIN OF ALTERED DOMAIN INTERACTIONS IN IMMUNOGLOBULIN LIGHT CHAIN DIMERS
ComponentsBENCE-JONES PROTEIN MCG (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / immunoglobulin complex / 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 / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / immunoglobulin complex / 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 / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular exosome / 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 1D-33 / Immunoglobulin kappa variable 1D-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHuang, D.B. / Chang, C.H. / Schiffer, M.
Citation
Journal: Biochemistry / Year: 1994
Title: Comparison of crystal structures of two homologous proteins: structural origin of altered domain interactions in immunoglobulin light-chain dimers.
Authors: Huang, D.B. / Chang, C.H. / Ainsworth, C. / Brunger, A.T. / Eulitz, M. / Solomon, A. / Stevens, F.J. / Schiffer, M.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Characterization and Preliminary Crystallographic Data on the Vl-Related Fragment of the Human Ki Bence-Jones Protein Wat
Authors: Stevens, F.J. / Westholm, F.A. / Panagiotopoulos, N. / Schiffer, M. / Popp, R.A. / Solomon, A.
#2: Journal: Biochemistry / Year: 1975
Title: The Molecular Structure of a Dimer Composed of the Variable Portions of the Bence-Jones Protein Rei Refined at 2.0 Angstroms Resolution
Authors: Schiffer, M. / Epp, O. / Lattman, E.E. / Schiffer, M. / Huber, R. / Palm, W.
History
DepositionJun 8, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)23,4902
Polymers23,4902
Non-polymers00
Water3,531196
1
A: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)

A: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,9804
Polymers46,9804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)82.250, 82.250, 61.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO B 8 / 4: CIS PROLINE - PRO B 95
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.58747, -0.30138, 0.75103), (-0.33404, -0.755, -0.56426), (0.73703, -0.58232, 0.34285)
Vector: -15.707, 72.652, 39.204)

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Components

#1: Antibody BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Mass: 11745.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P80362, UniProt: P01593*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
Conc.: 20 % / Common name: dextran

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.157 10320
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 196 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0420.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.741
X-RAY DIFFRACTIONp_mcangle_it1.291.5
X-RAY DIFFRACTIONp_scbond_it1.181.5
X-RAY DIFFRACTIONp_scangle_it1.82
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.1980.3
X-RAY DIFFRACTIONp_multtor_nbd0.2360.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2090.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor23.513
X-RAY DIFFRACTIONp_orthonormal_tor18.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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