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- PDB-1qp1: KAPPA VARIABLE LIGHT CHAIN -

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Basic information

Entry
Database: PDB / ID: 1qp1
TitleKAPPA VARIABLE LIGHT CHAIN
ComponentsBENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / BETA SANDWICH / DOUBLE SPIRAL
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 / immunoglobulin complex / 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 / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex / 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 / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular region / identical protein binding / 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 1-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSteinrauf, L.K.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1999
Title: Molecular structure of the amyloid-forming protein kappa I Bre.
Authors: Steinrauf, L.K. / Chiang, M.Y. / Shiuan, D.
#1: Journal: Am.Cryst.Assoc.,Abstr.Papers (Annual Meeting) / Year: 1993
Title: Structure of an Immunoglubulin Kappa Variable Light Chain Associated with Primary Amyloidosis
Authors: Steinrauf, L.K. / Hamilton, J.A. / Clawson, D. / Liepnieks, J. / Murrell, J. / Benson, M.D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Tertiary Structure of an Amyloid Immunoglobulin Light Chain Protein: A Proposed Model for Amyloid Fibril Formation
Authors: Schormann, N. / Murrell, J.R. / Liepnieks, J.R. / Benson, M.D.
History
DepositionMay 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 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: BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)
B: BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)
C: BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)35,3643
Polymers35,3643
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.990, 82.560, 77.560
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-165-

HOH

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Components

#1: Antibody BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)


Mass: 11787.930 Da / Num. of mol.: 3 / Fragment: IMMUNOGLOBULIN FRAGMENT, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BONE MARROW / Plasmid: PCZ11 / Production host: Escherichia coli (E. coli) / References: PIR: I39154, UniProt: P01594*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: AMMONIUM SULFATE, CITRATE BUFFER, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
260 %ammonium sulfate11
3200 mMcitrate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 11, 1992
RadiationMonochromator: BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→60 Å / Num. all: 89999 / Num. obs: 22485 / % possible obs: 68.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24
Reflection shellResolution: 2.06→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.92 / % possible all: 50.25
Reflection shell
*PLUS
% possible obs: 50.2 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE BENCE-JONES PROTEINS ROY: COLMAN, SCHRAMM, GURS J. MOL. BIOL. 116, 73, 1977 AND REI: EPP, COLMAN, FEHLHAMMER, BODE, SCHIFFER, HUBER, AND PALM EUR. J. BIOCHEM. 45, 513 1974

Resolution: 2.06→20 Å / Num. parameters: 1040 / Num. restraintsaints: 984 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2248 10 %10% CHOSEN AT RANDOM FROM LIST OF REFLECTIONS SORTED ON SIZE OF F.
Rwork0.153 ---
all0.183 32634 --
obs0.188 22485 68.9 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2708
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 0 191 2678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.001
X-RAY DIFFRACTIONs_from_restr_planes0.0169
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.017
X-RAY DIFFRACTIONs_chiral_restr0.093

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