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- PDB-2cd0: STRUCTURE OF HUMAN LAMBDA-6 LIGHT CHAIN DIMER WIL -

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Basic information

Entry
Database: PDB / ID: 2cd0
TitleSTRUCTURE OF HUMAN LAMBDA-6 LIGHT CHAIN DIMER WIL
ComponentsPROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / BENCE-JONES PROTEIN / LAMBDA-6
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 / 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 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 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPokkuluri, P.R. / Solomon, A. / Weiss, D.T. / Stevens, F.J. / Schiffer, M.
CitationJournal: Amyloid / Year: 1999
Title: Tertiary structure of human lambda 6 light chains.
Authors: Pokkuluri, P.R. / Solomon, A. / Weiss, D.T. / Stevens, F.J. / Schiffer, M.
History
DepositionMar 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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: PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
B: PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,0042
Polymers24,0042
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.900, 147.900, 46.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS A HOMODIMER. THE ASYMMETRIC UNIT CONTAINS BOTH MONOMERS, CHAINS A AND B. BOTH MONOMERS REFINED INDEPENDENTLY.

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Components

#1: Antibody PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)


Mass: 12001.915 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5LAMBDA / References: GenBank: 587410, UniProt: P01721*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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 Å3/Da / Density % sol: 38.5 %
Description: CONSTANT DOMAINS WERE ALSO REMOVED FROM MCG MODEL PRIOR TO MOLECULAR REPLACEMENT.
Crystal growpH: 5.6
Details: 1.8M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE PH 5.6, 0.01 M CADMIUM CHLORIDE
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 8.5 / PH range high: 4.6
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate1reservoir
2PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 21478 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 21.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 48
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 19 / % possible all: 96.4
Reflection shell
*PLUS
% possible obs: 96.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MCG (1DCL): USED ONLY VL DIMER WITH CDR LOOPS DELETED.

1dcl


Resolution: 1.8→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1379583.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.351 1689 9.8 %RANDOM
Rwork0.289 ---
obs-17271 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65 Å2 / ksol: 0.49 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å2-2.21 Å20 Å2
2---2.28 Å20 Å2
3---4.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 112 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.021.5
X-RAY DIFFRACTIONx_mcangle_it1.742
X-RAY DIFFRACTIONx_scbond_it1.162
X-RAY DIFFRACTIONx_scangle_it1.682.5
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.41 58 11.9 %
Rwork0.363 431 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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