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- PDB-1cd0: STRUCTURE OF HUMAN LAMDA-6 LIGHT CHAIN DIMER JTO -

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Basic information

Entry
Database: PDB / ID: 1cd0
TitleSTRUCTURE OF HUMAN LAMDA-6 LIGHT CHAIN DIMER JTO
ComponentsPROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / BENCE-JONES PROTEIN / LAMDA-6
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 phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / 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 phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / 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 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-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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda variable 6-57 / Immunoglobulin lambda variable 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
B: PROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1942
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.900, 60.500, 73.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICALLY ACTIVE MOLECULE IS A HOMODIMER. ASYMMETRIC UNIT CONTAINS BOTH MONOMERS, CHAINS A AND B. BOTH MONOMERS REFINED INDEPENDENTLY.

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Components

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


Mass: 12097.149 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06317, UniProt: P01721*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 38 %
Description: CONSTANT DOMAINS WERE ALSO DELETED FROM THE STARTING MODEL.
Crystal growpH: 6.5
Details: 27.5% PEG6000, 0.08 M SODIUM CACODYLATE PH 6.5, 0.1 M SODIUM ACETATE
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 15655 / % possible obs: 95 % / Redundancy: 4.87 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.3 / % possible all: 89.8
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

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

1dcl


Resolution: 1.9→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 362162.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1247 10.2 %RANDOM
Rwork0.184 ---
obs-12188 79.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.6 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 0 247 1917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.781.5
X-RAY DIFFRACTIONx_mcangle_it1.352
X-RAY DIFFRACTIONx_scbond_it1.042
X-RAY DIFFRACTIONx_scangle_it1.492.5
LS refinement shellResolution: 1.9→1.93 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.233 28 10 %
Rwork0.205 253 -
obs--46.7 %
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_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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