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- PDB-1eeu: M4L/Y(27D)D/Q89D/T94H mutant of LEN -

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Basic information

Entry
Database: PDB / ID: 1eeu
TitleM4L/Y(27D)D/Q89D/T94H mutant of LEN
ComponentsKAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / Human Kappa-4 Immunoglobulin Light Chain / Mutant / Aspartic Acid in beta-sheet / Protein Stability
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 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 / Initial triggering of complement / immunoglobulin complex / 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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / 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
ISOPROPYL ALCOHOL / Immunoglobulin kappa variable 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body fitting / 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 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 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: KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
B: KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3364
Polymers25,2162
Non-polymers1202
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.900, 104.800, 42.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological Assembly is a homo dimer formed by chains A and B.

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Components

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


Mass: 12607.890 Da / Num. of mol.: 2 / Mutation: M4L/Y(27D)D/Q89D/T94H
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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG4K, 20% 2-Propanol, 0.1 M Sodium Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
220 %2-propanol1reservoir
30.1 Msodium citrate1reservoirpH5.6
410 mg/mlprotein1drop
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91841
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 37837 / Num. obs: 37705 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 18 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 43.6
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.3 / Num. unique all: 3491 / % possible all: 99.6
Reflection shell
*PLUS
Rmerge(I) obs: 0.263

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: Rigid body fitting
Starting model: 1EEQ WITH ATOMS BEYOND CB REMOVED FOR RESIDUES A 89 AND B 389

1eeq


Resolution: 1.6→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 763311.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3465 10 %RANDOM
Rwork0.194 ---
all-37453 --
obs-34586 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.31 Å2 / ksol: 0.515 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2---1.68 Å20 Å2
3---4.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 342 2069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it0.491.5
X-RAY DIFFRACTIONc_mcangle_it0.872
X-RAY DIFFRACTIONc_scbond_it0.732
X-RAY DIFFRACTIONc_scangle_it1.132.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 482 10.2 %
Rwork0.204 4247 -
obs--76.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IPA.PARAMIPA.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.204

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