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- PDB-2lek: Solution NMR structure of a Thiamine Biosynthesis (ThiS) Protein ... -

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Basic information

Entry
Database: PDB / ID: 2lek
TitleSolution NMR structure of a Thiamine Biosynthesis (ThiS) Protein RPA3574 from Rhodopseudomonas palustris refined with NH RDCs. Northeast Structural Genomics Consortium target RpR325
ComponentsPutative thiamin biosynthesis ThiS
KeywordsBIOSYNTHETIC PROTEIN / beta-grasp fold / Structural Genomics / Northeast Structural Genomics Consortium / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Putative thiamin biosynthesis ThiS
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Cort, J.R. / Lee, H. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Ramelot, T.A. / Cort, J.R. / Lee, H. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of a Thiamine Biosynthesis (ThiS) Protein RPA3574 from Rhodopseudomonas palustris. Northeast Structural Genomics Consortium target RpR325
Authors: Ramelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionAug 24, 2011ID: 2KL0
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: Putative thiamin biosynthesis ThiS


Theoretical massNumber of molelcules
Total (without water)8,1091
Polymers8,1091
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative thiamin biosynthesis ThiS


Mass: 8108.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: thiS, RPA3574 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PMGK / References: UniProt: Q6N3W8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1422D 1H-13C HSQC-CT
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliph
1713D HNCO
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D 1H-13C NOESY arom
11113D HBHA(CO)NH
11213D C(CCO)NH
11313D (H)CCH-TOCSY
11433D CCH-TOCSY
11512D 1H-15N HSQC His
11613D HNCA
11713D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM U-100% 15N and 5% 13C biosynthetically directed protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMprotein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
10 mMDTT-61
0.8 mMprotein-7U-100% 15N and 5% 13C biosynthetically directed2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
0.9 mMprotein-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
0.02 %sodium azide-173
10 mMDTT-183
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.4(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
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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