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- PDB-2jtr: rhodanese persulfide from E. coli -

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Basic information

Entry
Database: PDB / ID: 2jtr
Titlerhodanese persulfide from E. coli
ComponentsPhage shock protein E
KeywordsTRANSFERASE / solution structure rhodanese persulfide / Stress response
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Phage shock protein, PspE / : / 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
Thiosulfate sulfurtransferase PspE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsJin, C. / Li, H.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.
Authors: Li, H. / Yang, F. / Kang, X. / Xia, B. / Jin, C.
History
DepositionAug 6, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 29, 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: Phage shock protein E


Theoretical massNumber of molelcules
Total (without water)9,4421
Polymers9,4421
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)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Phage shock protein E


Mass: 9441.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pspE / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P23857, thiosulfate sulfurtransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-15N HSQC
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CO)CA
11113D H(CCO)NH
11213D (H)CCH-TOCSY
11313D 1H-15N TOCSY
11413D (H)CCH-COSY
11513D HCACO

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] rhodanese persulfide, 20 mM sodium thiosulfate, 20 mM TRIS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMrhodanese persulfide[U-13C; U-15N]1
20 mMsodium thiosulfate1
20 mMTRIS1
Sample conditionsIonic strength: 0.04 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
Amber7Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichinitial structure calculation
DYANAGuntert, Braun and Wuthrichstructure calculation
MOLMOLKoradi, Billeter and Wuthrichgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
SANEDuggan, Legge, Dyson & Wrightchemical shift calculation
TALOSCornilescu, Delaglio and Baxangle restraints
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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