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- PDB-8xkk: Ckappa domain of mouse immunoglobulin -

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Basic information

Entry
Database: PDB / ID: 8xkk
TitleCkappa domain of mouse immunoglobulin
ComponentsImmunoglobulin kappa constant
KeywordsIMMUNE SYSTEM / STRUCTURE FROM CYANA 3.98.15
Function / homology
Function and homology information


B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry
AuthorsYanaka, S. / Kodama, A. / Miyanoiri, Y. / Kato, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H02755 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121020h0001 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121013h0301 Japan
CitationJournal: Int.Immunol. / Year: 2024
Title: Identification of potential C1-binding sites in the immunoglobulin CL domains.
Authors: Yanaka, S. / Kodama, A. / Nishiguchi, S. / Fujita, R. / Shen, J. / Boonsri, P. / Sung, D. / Isono, Y. / Yagi, H. / Miyanoiri, Y. / Uchihashi, T. / Kato, K.
History
DepositionDec 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin kappa constant


Theoretical massNumber of molelcules
Total (without water)12,5691
Polymers12,5691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Immunoglobulin kappa constant / Ig kappa chain C region MOPC 21


Mass: 12568.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igkc / Production host: Escherichia coli (E. coli) / References: UniProt: P01837
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D C(CO)NH
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HCACO
161isotropic13D HNCO
171isotropic13D HN(CO)CA
181isotropic13D HNCA
191isotropic13D HBHA(CO)NH
1101isotropic13D CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY
1131isotropic13D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.6 mM [U-13C; U-15N] Ckappa domain of mouse immunoglobulin, 5 mM NaPi, 50 mM sodium chloride, 95% H2O/5% D2O13C, 15N95% H2O/5% D2O
solution31.6 mM [U-13C; U-15N] Ckappa domain of mouse immunoglobulin, 95% H2O/5% D2O13C, 15N95% H2O/5% D2O
solution21.6 mM [U-13C; U-15N] Ckappa domain of mouse immunoglobulin, 95% H2O/5% D2O13C, 15N95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMCkappa domain of mouse immunoglobulin[U-13C; U-15N]1
5 mMNaPinone1
50 mMsodium chloridenone1
1.6 mMCkappa domain of mouse immunoglobulin[U-13C; U-15N]3
1.6 mMCkappa domain of mouse immunoglobulin[U-13C; U-15N]2
Sample conditionsIonic strength: Not defined Not defined / Label: condition_1 / pH: 6 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
ARTINAKlukowski, P., Riek, R. and Guntert, P.refinement
ARTINAKlukowski, P., Riek, R. and Guntert, P.structure calculation
ARTINAKlukowski, P., Riek, R. and Guntert, P.chemical shift assignment
ARTINAKlukowski, P., Riek, R. and Guntert, P.peak picking
RefinementMethod: distance geometry / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 20

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