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- PDB-2moi: 3D NMR structure of the cytoplasmic rhodanese domain of the inner... -

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Basic information

Entry
Database: PDB / ID: 2moi
Title3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli
ComponentsInner membrane protein YgaP
KeywordsMEMBRANE PROTEIN / Rhodanese domain
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / plasma membrane
Similarity search - Function
Inner membrane protein YgaP-like, transmembrane domain / Inner membrane protein YgaP-like, transmembrane domain / 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 YgaP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 10
AuthorsEichmann, C. / Tzitzilonis, C. / Bordignon, E. / Maslennikov, I. / Choe, S. / Riek, R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP from Escherichia coli.
Authors: Eichmann, C. / Tzitzilonis, C. / Bordignon, E. / Maslennikov, I. / Choe, S. / Riek, R.
History
DepositionApr 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein YgaP


Theoretical massNumber of molelcules
Total (without water)11,7161
Polymers11,7161
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)10 / 100target function
RepresentativeModel #10fewest violations

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Components

#1: Protein Inner membrane protein YgaP


Mass: 11716.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2668, JW2643, ygaP, ygaP b2668 JW2643 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS Star / References: UniProt: P55734

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CO)CA
1313D HNCA
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-15N TOCSY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] YgaP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAHerrmann, Guntert and Wuthrichchemical shift assignment
CYANAHerrmann, Guntert and Wuthrichstructure solution
CYANAHerrmann, Guntert and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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