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- PDB-2l16: Solution structure of Bacillus subtilits TatAd protein in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2l16
TitleSolution structure of Bacillus subtilits TatAd protein in DPC micelles
ComponentsSec-independent protein translocase protein tatAd
KeywordsPROTEIN TRANSPORT / membrane protein
Function / homology
Function and homology information


TAT protein transport complex / protein transport by the Tat complex / plasma membrane => GO:0005886 / protein transmembrane transporter activity / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3310 / Sec-independent protein translocase protein TatA/B/E / Sec-independent protein translocase protein TatA/E / mttA/Hcf106 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Sec-independent protein translocase protein TatAd
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHu, Y. / Jin, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Solution NMR structure of the TatA component of the twin-arginine protein transport system from gram-positive bacterium Bacillus subtilis
Authors: Hu, Y. / Zhao, E. / Li, H. / Xia, B. / Jin, C.
History
DepositionJul 23, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sec-independent protein translocase protein tatAd


Theoretical massNumber of molelcules
Total (without water)8,5111
Polymers8,5111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 200structures with lowest energy as well as good correlation with RDC data
RepresentativeModel #1lowest energy

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Components

#1: Protein Sec-independent protein translocase protein tatAd


Mass: 8510.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tatAd, yczB, BSU02630 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31467

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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-15N HSQC
1322D 1H-13C HSQC
1423D HNCA
1523D HNCO
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D HBHA(CO)NH
1923D C(CO)NH
11023D H(CCO)NH
11123D (H)CCH-COSY
11223D (H)CCH-TOCSY
11323D 1H-15N NOESY
11423D 1H-13C NOESY
11523D HN(CA)CO
21632D 1H-15N IPAP
21742D 1H-15N IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] TatAd-1, 90 % H2O-2, 10 % D2O-3, 0.01 % DSS-4, 50 mM sodium phosphate-5, 5 % DPC-6, 0.01 % sodium azide-7, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] TatAd-8, 90 % H2O-9, 10 % D2O-10, 0.01 % DSS-11, 50 mM sodium phosphate-12, 5 % [U-2H] DPC-13, 0.01 % sodium azide-14, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-15N] TatAd-15, 90 % H2O-16, 10 % D2O-17, 100 mM potassium phosphate-18, 5 % DPC-19, 0.01 % sodium azide-20, 9.0 mg in up to 500 ul G-tetra DNA-21, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-15N] TatAd-22, 90 % H2O-23, 10 % D2O-24, 100 mM potassium phosphate-25, 5 % DPC-26, 0.01 % sodium azide-27, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTatAd-1[U-15N]1
90 %H2O-21
10 %D2O-31
0.01 %DSS-41
50 mMsodium phosphate-51
5 %DPC-61
0.01 %sodium azide-71
1 mMTatAd-8[U-13C; U-15N]2
90 %H2O-92
10 %D2O-102
0.01 %DSS-112
50 mMsodium phosphate-122
5 %DPC-13[U-2H]2
0.01 %sodium azide-142
1 mMTatAd-15[U-15N]3
90 %H2O-163
10 %D2O-173
100 mMpotassium phosphate-183
5 %DPC-193
0.01 %sodium azide-203
18 mg/mLG-tetra DNA-213
1 mMTatAd-22[U-15N]4
90 %H2O-234
10 %D2O-244
100 mMpotassium phosphate-254
5 %DPC-264
0.01 %sodium azide-274
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.3 7.0 ambient 298 K
20.6 7.0 ambient 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest energy as well as good correlation with RDC data
Conformers calculated total number: 200 / Conformers submitted total number: 40 / Representative conformer: 1

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