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- PDB-2mmx: NMR study of 6aJL2 -

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Basic information

Entry
Database: PDB / ID: 2mmx
TitleNMR study of 6aJL2
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 detailsany, model1
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
DepositionMar 20, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Jun 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)11,9621
Polymers11,9621
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 #1any

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Components

#1: Antibody V1-22 protein


Mass: 11961.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: V1-22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D HNCA
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1723D 1H-13C NOESY aliphatic
1823D CBCA(CO)NH
1923D HNCO
11023D (H)CCH-TOCSY
11123D HCACO

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate-1, 75 mM sodium chloride-2, 5 % D2O-3, 1 mM [U-100% 15N] 6aJL2-4, 95% H2O/5% D2O95% H2O/5% D2O
250 mM sodium phosphate-5, 75 mM sodium chloride-6, 5 % D2O-7, 1 mM [U-100% 13C; U-100% 15N] 6aJL2-8, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
75 mMsodium chloride-21
5 %D2O-31
1 mM6aJL2-4[U-100% 15N]1
50 mMsodium phosphate-52
75 mMsodium chloride-62
5 %D2O-72
1 mM6aJL2-8[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 75 / pH: 7.4 / Pressure: ambient atm / Temperature: 298 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: 1216 / NOE intraresidue total count: 535 / NOE long range total count: 317 / NOE medium range total count: 81 / NOE sequential total count: 283 / Hydrogen bond constraints total count: 31
NMR representativeSelection criteria: any
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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