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- PDB-5xp1: Structure of monomeric mutant of REI immunoglobulin light chain v... -

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Basic information

Entry
Database: PDB / ID: 5xp1
TitleStructure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6
ComponentsImmunoglobulin kappa variable 1D-33
KeywordsIMMUNE SYSTEM / Immunoglobulin
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 LAT2/NTAL/LAB on calcium mobilization / 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 / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular exosome / 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 / 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 1D-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsMine, S. / Nakamura, T. / Uegaki, K. / Hamada, D.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS26440076 Japan
JSPS23107721 Japan
CitationJournal: FEBS J. / Year: 2017
Title: Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI
Authors: Nawata, M. / Tsutsumi, H. / Kobayashi, Y. / Unzai, S. / Mine, S. / Nakamura, T. / Uegaki, K. / Kamikubo, H. / Kataoka, M. / Hamada, D.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 2, 2017ID: 5B3C
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Mar 12, 2025Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin kappa variable 1D-33
B: Immunoglobulin kappa variable 1D-33
C: Immunoglobulin kappa variable 1D-33
D: Immunoglobulin kappa variable 1D-33
E: Immunoglobulin kappa variable 1D-33
F: Immunoglobulin kappa variable 1D-33
G: Immunoglobulin kappa variable 1D-33
H: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)95,5708
Polymers95,5708
Non-polymers00
Water21612
1
A: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Immunoglobulin kappa variable 1D-33


Theoretical massNumber of molelcules
Total (without water)11,9461
Polymers11,9461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.760, 130.760, 92.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Antibody
Immunoglobulin kappa variable 1D-33 / Ig kappa chain V-I region AG / Ig kappa chain V-I region Bi / Ig kappa chain V-I region Lay / Ig ...Ig kappa chain V-I region AG / Ig kappa chain V-I region Bi / Ig kappa chain V-I region Lay / Ig kappa chain V-I region Ni / Ig kappa chain V-I region Rei / Ig kappa chain V-I region Roy / Ig kappa chain V-I region Scw / Ig kappa chain V-I region WAT


Mass: 11946.266 Da / Num. of mol.: 8 / Fragment: UNP residues 22-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKV1D-33 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01593
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAuthors state that the structure was based on the sequence of UNP P01607 as well as the structure ...Authors state that the structure was based on the sequence of UNP P01607 as well as the structure 1REI, which is updated by P01593 at present. Therefore, the structure has a mutation Y96K. Other conflicts are due to sequence conflicts of P01607.

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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: 4.22 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M BIS-TRIS pH 6.0, 18% POLYETHYLENE GLYCOL 3350, 0.12M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→17.961 Å / Num. obs: 35217 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 65.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.3
Reflection shellResolution: 2.88→2.93 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 5 / Num. unique obs: 5153 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
iMOSFLMV7.0.9data reduction
SCALAV3.3.20data scaling
MOLREPV11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q20

2q20


Resolution: 2.88→17.961 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 1763 5.01 %
Rwork0.2567 --
obs0.2588 35191 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→17.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 0 12 6669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046797
X-RAY DIFFRACTIONf_angle_d0.9379249
X-RAY DIFFRACTIONf_dihedral_angle_d5.9554098
X-RAY DIFFRACTIONf_chiral_restr0.0511045
X-RAY DIFFRACTIONf_plane_restr0.0051197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.98250.38691600.33773376X-RAY DIFFRACTION100
2.9825-3.10140.41741770.33953291X-RAY DIFFRACTION100
3.1014-3.24170.39651650.32533317X-RAY DIFFRACTION100
3.2417-3.41150.37381820.32493333X-RAY DIFFRACTION100
3.4115-3.62360.35291910.31643336X-RAY DIFFRACTION100
3.6236-3.90080.28961790.28683327X-RAY DIFFRACTION100
3.9008-4.28850.30751750.24613328X-RAY DIFFRACTION100
4.2885-4.8980.23321880.21073333X-RAY DIFFRACTION100
4.898-6.130.26891750.2243381X-RAY DIFFRACTION100
6.13-17.96160.24721710.2093406X-RAY DIFFRACTION99

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