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- PDB-2k1h: Solution NMR structure of SeR13 from Staphylococcus epidermidis. ... -

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Basic information

Entry
Database: PDB / ID: 2k1h
TitleSolution NMR structure of SeR13 from Staphylococcus epidermidis. Northeast Structural Genomics Consortium target SeR13
ComponentsUncharacterized protein SeR13
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Scaffold protein Nfu/NifU, N-terminal domain / Scaffold protein Nfu/NifU, N-terminal / Scaffold protein Nfu/NifU, N-terminal domain superfamily / Scaffold protein Nfu/NifU N terminal / Scaffold protein Nfu/NifU N terminal / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsThe oligomeric states of the SeR13 were verified by pulsed-field-gradient diffusion, dynamic light ...The oligomeric states of the SeR13 were verified by pulsed-field-gradient diffusion, dynamic light scattering, sedimentation equilibrium, and concentration dependent studies. The results indicated that the SeR13 self-associates weakly at protein concentration below 1 mM. Using the residual dipolar couplings as well as chemical shift perturbations on dilution, we constructed dimeric models for SeR13. Possible inter-subunit NOEs were identified based on these models. In cases where corresponding NOEs were observed, they were eliminated as constraints and the protein structure recalculated. The absence of structural variation and the failure to observed other predicted inter-subunit NOEs validated use of all NOEs as intra-subunit constraints.
AuthorsLee, H. / Wylie, G. / Bansal, S. / Wang, X. / Shastry, R. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. ...Lee, H. / Wylie, G. / Bansal, S. / Wang, X. / Shastry, R. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of SeR13.
Authors: Lee, H. / Wylie, G. / Bansal, S. / Montelione, G.T. / Prestegard, J.H.
History
DepositionMar 5, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 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: Uncharacterized protein SeR13


Theoretical massNumber of molelcules
Total (without water)10,9631
Polymers10,9631
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)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Uncharacterized protein SeR13


Mass: 10963.061 Da / Num. of mol.: 1 / Mutation: S28F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_1124 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8CSK1, UniProt: A0A0H2VGF1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The oligomeric states of the SeR13 were verified by pulsed-field-gradient diffusion, dynamic light scattering, sedimentation equilibrium, and concentration dependent studies. The results ...Details: The oligomeric states of the SeR13 were verified by pulsed-field-gradient diffusion, dynamic light scattering, sedimentation equilibrium, and concentration dependent studies. The results indicated that the SeR13 self-associates weakly at protein concentration below 1 mM. Using the residual dipolar couplings as well as chemical shift perturbations on dilution, we constructed dimeric models for SeR13. Possible inter-subunit NOEs were identified based on these models. In cases where corresponding NOEs were observed, they were eliminated as constraints and the protein structure recalculated. The absence of structural variation and the failure to observed other predicted inter-subunit NOEs validated use of all NOEs as intra-subunit constraints.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-15N TOCSY
11113D 1H-13C NOESY
11222D 1H-15N HSQC-TROSY
11332D 1H-15N HSQC-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.07 mM [U-100% 13C; U-100% 15N] SeR13, 0.2 % sodium azide, 100 mM DTT, 5 mM CaCl2, 100 mM sodium chloride, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
20.86 mM [U-100% 13C; U-100% 15N] SeR13, 0.2 % sodium azide, 100 mM DTT, 5 mM CaCl2, 100 mM sodium chloride, 20 mM MES, 7 % Negative Charged Poly Acrylamide Compressed Gel, 95% H2O/5% D2O95% H2O/5% D2O
30.60 mM [U-100% 13C; U-100% 15N] SeR13, 0.2 % sodium azide, 100 mM DTT, 5 mM CaCl2, 100 mM sodium chloride, 20 mM MES, 7.5 % DMPS/DHPC Mixture, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.07 mMSeR13[U-100% 13C; U-100% 15N]1
0.2 %sodium azide1
100 mMDTT1
5 mMCaCl21
100 mMsodium chloride1
20 mMMES1
0.86 mMSeR13[U-100% 13C; U-100% 15N]2
0.2 %sodium azide2
100 mMDTT2
5 mMCaCl22
100 mMsodium chloride2
20 mMMES2
7 %Negative Charged Poly Acrylamide Compressed Gel2
0.60 mMSeR13[U-100% 13C; U-100% 15N]3
0.2 %sodium azide3
100 mMDTT3
5 mMCaCl23
100 mMsodium chloride3
20 mMMES3
7.5 %DMPS/DHPC Mixture3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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