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- PDB-1eeq: M4L/Y(27D)D/T94H Mutant of LEN -

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Basic information

Entry
Database: PDB / ID: 1eeq
TitleM4L/Y(27D)D/T94H Mutant of LEN
ComponentsKAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / Human Kappa-4 Immunoglobulin Light chain / Protein Stability / Hydrogen Bonds
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
Immunoglobulin kappa variable 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPokkuluri, P.R. / Raffen, R. / Dieckman, L. / Boogaard, C. / Stevens, F.J. / Schiffer, M.
CitationJournal: Biophys.J. / Year: 2002
Title: Increasing protein stability by polar surface residues: domain-wide consequences of interactions within a loop.
Authors: Pokkuluri, P.R. / Raffen, R. / Dieckman, L. / Boogaard, C. / Stevens, F.J. / Schiffer, M.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
B: KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)25,2422
Polymers25,2422
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 105.200, 42.300
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: 12620.931 Da / Num. of mol.: 2 / Mutation: M4L/Y(27D)D/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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 10% 2-propanol, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG33501reservoir
210 %2-propanol1reservoir
30.1 Msodium HEPES1reservoir
410 mg/mlprotein1drop

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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 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 45022 / Num. obs: 44489 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 17 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 46.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.6 / Num. unique all: 4271 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3Crefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVE. Dimer generated by crystallographic operation. Atoms beyond CB removed for mutated residues.

1lve


Resolution: 1.5→7.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1244368.97 / 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
Rfree0.238 4211 10.1 %RANDOM
Rwork0.211 ---
obs0.211 41633 92.1 %-
all-45151 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.82 Å2 / ksol: 0.503 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å20 Å2
2---1.17 Å20 Å2
3---3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 361 2098
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_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it0.631.5
X-RAY DIFFRACTIONc_mcangle_it1.092
X-RAY DIFFRACTIONc_scbond_it1.032
X-RAY DIFFRACTIONc_scangle_it1.552.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 589 10.5 %
Rwork0.22 5030 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.7 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_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
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: 0.255 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.22

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