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- PDB-1f0z: SOLUTION STRUCTURE OF THIS, THE SULFUR CARRIER PROTEIN IN E.COLI ... -

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Basic information

Entry
Database: PDB / ID: 1f0z
TitleSOLUTION STRUCTURE OF THIS, THE SULFUR CARRIER PROTEIN IN E.COLI THIAMIN BIOSYNTHESIS
ComponentsTHIS PROTEIN
KeywordsTRANSPORT PROTEIN / Ubiquitin fold
Function / homology
Function and homology information


adenylyltransferase complex / sulfurtransferase complex / thiazole biosynthetic process / sulfur carrier activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotide binding
Similarity search - Function
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
Sulfur carrier protein ThiS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsWang, C. / Xi, J. / Begley, T.P. / Nicholson, L.K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Solution structure of ThiS and implications for the evolutionary roots of ubiquitin.
Authors: Wang, C. / Xi, J. / Begley, T.P. / Nicholson, L.K.
History
DepositionMay 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,3151
Polymers7,3151
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)24 / 30structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein THIS PROTEIN


Mass: 7315.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SULFUR CARRIER PROTEIN / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCLK413 / Production host: Escherichia coli (E. coli) / References: UniProt: O32583

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1243D 13C-separated NOESY
1333D 13C-separated NOESY
1412D NOESY
152HNHA
162HMQC-J
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM ThiS NA; 25 mM sodium phosphate, 5 mM DTT, 5 mg/ml pepstatin, 50 microM EDTA, 50 microM chloramphenicol93% H2O/7% D2O
21 mM ThiS U-15N; 25 mM sodium phosphate, 5 mM DTT, 5 mg/ml pepstatin, 50 microM EDTA, 50 microM chloramphenicol93% H2O/7% D2O
31 mM ThiS U-15N, 13C; 25 mM sodium phosphate, 5 mM DTT, 5 mg/ml pepstatin, 50 microM EDTA, 50 microM chloramphenicol93% H2O/7% D2O
41 mM ThiS U-15N, 13C; 25 mM sodium phosphate, 5 mM DTT, 5 mg/ml pepstatin, 50 microM EDTA, 50 microM chloramphenicol100% D2O
Sample conditionsIonic strength: 25 mM sodium phosphate / pH: 6.6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
VNMR6.1BVarian Associatescollection
NMRPipe1.7Delaglioprocessing
PIPP1Delagliodata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 882 restraints, 802 are NOE-derived distance constraints, 64 dihedral angle restraints, 16 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 24

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