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- PDB-2mkw: Solution Structure of 6aJl2 and 6aJL2-R24G Amyloidogenics Light C... -

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Basic information

Entry
Database: PDB / ID: 2mkw
TitleSolution Structure of 6aJl2 and 6aJL2-R24G Amyloidogenics Light Chain Proteins
ComponentsV1-22 protein
KeywordsIMMUNE SYSTEM / light chain / amyloidosis / systemic / lambda
Function / homology
Function and homology information


immune response / extracellular space
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model3
AuthorsAmero, C. / Maya-Martinez, R.C. / Gil-Rodriguez, P.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Solution structure of 6aJL2 and 6aJL2-R24G amyloidogenics light chain proteins.
Authors: Maya-Martinez, R. / Gil-Rodriguez, P. / Amero, C.
History
DepositionFeb 13, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V1-22 protein


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody V1-22 protein


Mass: 11861.768 Da / Num. of mol.: 1 / Mutation: R24G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: V1-22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NV88

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D 1H-13C NOESY
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1613D HNCA
1713D HNCO
1813D HN(CO)CA
NMR detailsText: The structure was calculated using a combination of the HN-HSQC, HN-NOESY, D2O-HSQC, SEA-HSQC experiments

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 75 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-100% 13C; U-100% 15N]11
50 mMsodium phosphate-21
75 mMsodium chloride-31
Sample conditionsIonic strength: 75 / pH: 7.4 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARARochus L.J. Kellerchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1343 / NOE intraresidue total count: 471 / NOE long range total count: 396 / NOE medium range total count: 77 / NOE sequential total count: 399 / Hydrogen bond constraints total count: 31
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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