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- PDB-6iwj: A designed domain swapped dimer -

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Basic information

Entry
Database: PDB / ID: 6iwj
TitleA designed domain swapped dimer
ComponentsArcheal Protein MK0293
KeywordsUNKNOWN FUNCTION / Complex / Domain-swapping / Archea / Protein design
Function / homologyNickel insertion protein / Nickel insertion protein / Uncharacterized conserved protein
Function and homology information
Biological speciesMethanopyrus kandleri AV19 (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsNandwani, N. / Negi, H. / Das, R.
CitationJournal: Nat Commun / Year: 2019
Title: A five-residue motif for the design of domain swapping in proteins.
Authors: Nandwani, N. / Surana, P. / Negi, H. / Mascarenhas, N.M. / Udgaonkar, J.B. / Das, R. / Gosavi, S.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archeal Protein MK0293
B: Archeal Protein MK0293


Theoretical massNumber of molelcules
Total (without water)22,6482
Polymers22,6482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3920 Å2
ΔGint-20 kcal/mol
Surface area11640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Archeal Protein MK0293


Mass: 11323.766 Da / Num. of mol.: 2 / Mutation: Y109Q/G110V/E111V/R112A/E113G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri AV19 (archaea) / Gene: MK0293 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TYK3

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
191isotropic13D HNCO
181isotropic13D HN(CO)CA
171isotropic13D (H)CCH-TOCSY
161isotropic13D HN(CA)CB
1101isotropic13D 1H-15N TOCSY
1131isotropic13D HBHA(CO)NH
1121isotropic13D HN(CA)CO
1111isotropic13D 1H-15N NOESY
1151isotropic13D 1H-13C NOESY
1142isotropic13D Filtered NOESY
1162isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-13C; U-15N] Archeal Protein MK0293, 20 mM TRIS, 90% H2O/10% D2O15N,13C sample90% H2O/10% D2O
solution20.7 mM [U-13C; U-15N] Archeal Protein MK0293-1, 0.7 mM Archeal Protein MK0293-2, 20 mM TRIS, 90% H2O/10% D2OLabeled-Unlabeled dimer90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMArcheal Protein MK0293[U-13C; U-15N]1
20 mMTRISnatural abundance1
0.7 mMArcheal Protein MK0293-1[U-13C; U-15N]2
0.7 mMArcheal Protein MK0293-2natural abundance2
20 mMTRISnatural abundance2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
SparkyGoddardchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOSCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
Refinement
MethodSoftware ordinal
simulated annealing4
simulated annealing5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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