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- PDB-1efq: Q38D mutant of LEN -

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Basic information

Entry
Database: PDB / ID: 1efq
TitleQ38D mutant of LEN
ComponentsKAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / Human Kappa-4 Immunoglobulin Light Chain / Mutant / Monomer / Uranyl ion in crystal contact / Aspartic Acid in beta-sheet / Protein Stability
Function / homology
Function and homology information


CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / 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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 / blood microparticle / 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
URANYL (VI) ION / Immunoglobulin kappa variable 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsPokkuluri, P.R. / Cai, X. / Gu, M. / Stevens, F.J. / Schiffer, M.
CitationJournal: Protein Sci. / Year: 2002
Title: Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions.
Authors: Pokkuluri, P.R. / Gu, M. / Cai, X. / Raffen, R. / Stevens, F.J. / Schiffer, M.
History
DepositionFeb 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9723
Polymers12,6371
Non-polymers3352
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.8, 65.8, 48.1
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number173
Space group name H-MP63
DetailsNative Len is a homo-dimer, Whereas the Q38D mutant reported in this entry appears to be a monomer in the crystal. In solution, the association constant of Q38D is 66 times lower than the native Len.

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Components

#1: Antibody KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)


Mass: 12636.971 Da / Num. of mol.: 1 / Mutation: Q38D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PASK40 / Production host: Escherichia coli (E. coli) / References: UniProt: P01625, UniProt: P06312*PLUS
#2: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNative Len is a homo-dimer, whereas the Q38D mutant reported in this entry appears to be a monomer ...Native Len is a homo-dimer, whereas the Q38D mutant reported in this entry appears to be a monomer in the crystal. In solution, the association constant of Q38D is 66 times lower than the native Len.

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG monomethylether 550, 0.01 M zinc sulfate, 0.1 M MES pH 6.5, 0.001M Uranyl Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG550 MME1reservoir
20.01 Mzinc sulfate1reservoir
30.1 MMES1reservoirpH6.5
41 mMuranyl acetate1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 15773 / Num. obs: 15317 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 16 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.204 / Num. unique all: 1009 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 1.6→8 Å / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
Details: Due to the presence of uranyl ion in the crystal there is significant anomalous contribution to the diffraction at 1 Angstrom wavelength. When Friedel pairs are not averaged, the anomalous ...Details: Due to the presence of uranyl ion in the crystal there is significant anomalous contribution to the diffraction at 1 Angstrom wavelength. When Friedel pairs are not averaged, the anomalous difference Patterson map calculated clearly showed the position of uranium atom. Using the anomalous data the final model has an R-factor of 0.231 and R-free of 0.264. THE ELECTRON DENSITY INDICATED ANISOROPIC MOTION OF THE URANIUM ATOM. THE POSITIONS OF URANYL OXYGENS WERE NOT CLEAR IN THE ELECTRON DENSITY MAPS. THE OXYGEN ATOMS WERE PLACED ACCORDING TO THE EXPECTED GEOMETRY AROUND THE URANIUM ATOM AND SEEM TO IMPROVE BOTH R-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1471 -RANDOM
Rwork0.2303 ---
all-15121 --
obs-14410 10 %-
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms857 0 4 101 962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.57
X-RAY DIFFRACTIONx_torsion_deg28.3
X-RAY DIFFRACTIONx_torsion_impr_deg1.3
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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