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- PDB-1yx3: NMR structure of Allochromatium vinosum DsrC: Northeast Structura... -

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Basic information

Entry
Database: PDB / ID: 1yx3
TitleNMR structure of Allochromatium vinosum DsrC: Northeast Structural Genomics Consortium target OP4
Componentshypothetical protein DsrC
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DsrC / Dissimilatory sulfite reductase / gamma subunit / DsvC / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfurtransferases / sulfur carrier activity / tRNA wobble position uridine thiolation / transferase activity / cytoplasm
Similarity search - Function
DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Arc Repressor Mutant, subunit A / 2-Layer Sandwich ...DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAllochromatium vinosum (bacteria)
MethodSOLUTION NMR
AuthorsCort, J.R. / Dahl, C. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Allochromatium vinosum DsrC: solution-state NMR structure, redox properties, and interaction with DsrEFH, a protein essential for purple sulfur bacterial sulfur oxidation.
Authors: Cort, J.R. / Selan, U. / Schulte, A. / Grimm, F. / Kennedy, M.A. / Dahl, C.
#1: Journal: J.Bacteriol. / Year: 2005
Title: Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum.
Authors: Dahl, C. / Engels, S. / Pott-Sperling, A.S. / Schulte, A. / Sander, J. / Lubbe, Y. / Deuster, O. / Brune, D.C.
#2: Journal: MICROBIOLOGY / Year: 1998
Title: Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur.
Authors: Pott, A.S. / Dahl, C.
History
DepositionFeb 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein DsrC


Theoretical massNumber of molelcules
Total (without water)14,7921
Polymers14,7921
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)20 / 25low energy structures with fewest restraint violations
RepresentativeModel #1low energy, few violations, close to average structure

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Components

#1: Protein hypothetical protein DsrC


Mass: 14791.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Gene: DsrC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87899

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13N,15N-separated simultaneous NOESY
1324D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-13C, 15N DsrC, 500 mM NaCl, 50 mM sodium phosphate, 5 mM DTT90% H2O/10% D2O
21 mM U-13C, 15N DsrC, 500 mM NaCl, 50 mM sodium phosphate, 5 mM DTT100% D2O
Sample conditionsIonic strength: 500 mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-XplorBrunger,Clore,Kuszewski,Schwieters,Tjandrarefinement
Sparky3.106T.D. Goddard, D.G. Knellerdata analysis
AutoStructure2.1.0G.T. Montelione, J.Y. Huangstructure solution
TALOS2003G. Cornilescu, F. Delaglio, A. Baxdata analysis
NMR representativeSelection criteria: low energy, few violations, close to average structure
NMR ensembleConformer selection criteria: low energy structures with fewest restraint violations
Conformers calculated total number: 25 / Conformers submitted total number: 20

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