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- PDB-1qxn: Solution Structure of the 30 kDa Polysulfide-sulfur Transferase H... -

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Basic information

Entry
Database: PDB / ID: 1qxn
TitleSolution Structure of the 30 kDa Polysulfide-sulfur Transferase Homodimer from Wolinella Succinogenes
Componentssulfide dehydrogenase
KeywordsTRANSFERASE / POLYSULFIDE-SULFUR TRANSFERASE / SUD / HOMODIMER
Function / homology
Function and homology information


: / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PENTASULFIDE-SULFUR / Sulfide dehydrogenase
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodSOLUTION NMR / Simulated annealing with torsion angle dynamics
AuthorsLin, Y.J. / Dancea, F. / Loehr, F. / Klimmek, O. / Pfeiffer-Marek, S. / Nilges, M. / Wienk, H. / Kroeger, A. / Rueterjans, H.
CitationJournal: Biochemistry / Year: 2004
Title: Solution Structure of the 30 kDa Polysulfide-Sulfur Transferase Homodimer from Wolinella succinogenes
Authors: Lin, Y.J. / Dancea, F. / Loehr, F. / Klimmek, O. / Pfeiffer-Marek, S. / Nilges, M. / Wienk, H. / Kroeger, A. / Rueterjans, H.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sulfide dehydrogenase
B: sulfide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0364
Polymers30,7152
Non-polymers3212
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 / 100target function
RepresentativeModel #8closest to the average

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Components

#1: Protein sulfide dehydrogenase / sud


Mass: 15357.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Plasmid: pQE60_Sud-HIS6 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q56748
#2: Chemical ChemComp-PS5 / PENTASULFIDE-SULFUR


Mass: 160.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: S5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1334D 15N/15N-separated NOESY
1443D CT CH3 13C-separated NOESY
1553D 13C-separated NOESY
166[15N-1H]-TROSY
1773D 15N-separated NOESY
1884D CT J-resolved 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Sud NA, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 100% D2O100% D2O
21mM Sud U-15N, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 95% H2O, 5% D2O95% H2O/5% D2O
31mM Sud U-2H,15N, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 95% H2O, 5% D2O95% H2O/5% D2O
41mM Sud U-15N,13C, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 95% H2O, 5% D2O95% H2O/5% D2O
51mM Sud U-15N,13C, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 100% D2O100% D2O
60.55 mM U-15N, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 6% w/v C8E5/n-octanol (1:0.87), 90% H2O, 10% D2O6% w/v C8E5/n-octanol (1:0.87), 90% H2O, 10% D2O
71mM Sud 50% asym. U-2H,15N, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 95% H2O, 5% D2O95% H2O/5% D2O
81mM Sud 50% asym. U-13C, 50mM sodium phosphate NA, 1mM polysulfide NA, 13mM sulfide NA, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: less than 100mM / pH: 7.6 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
AURELIA97Brukerdata analysis
NMRPipe1.6Delaglioprocessing
CNS1.1Brungerstructure solution
ARIA1.1Nilgesstructure solution
ARIA1.1Nilgesrefinement
RefinementMethod: Simulated annealing with torsion angle dynamics / Software ordinal: 1
Details: The final structures were refined in explicit solvent (water)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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