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- PDB-2mpn: 3D NMR structure of the transmembrane domain of the full-length i... -

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Basic information

Entry
Database: PDB / ID: 2mpn
Title3D NMR structure of the transmembrane domain of the full-length inner membrane protein YgaP from Escherichia coli
ComponentsInner membrane protein YgaP
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity / plasma membrane
Similarity search - Function
Helix Hairpins - #1340 / Inner membrane protein YgaP-like, transmembrane domain / Inner membrane protein YgaP-like, transmembrane domain / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Inner membrane protein 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
DepositionMay 29, 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 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein YgaP
B: Inner membrane protein YgaP


Theoretical massNumber of molelcules
Total (without water)14,3152
Polymers14,3152
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)10 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Inner membrane protein YgaP


Mass: 7157.496 Da / Num. of mol.: 2
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 HNCA
1313D HN(CO)CA
1413D 1H-15N NOESY
2522D 1H-15N HSQC
2623D 1H-15N NOESY
2723D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] YgaP, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-100% 13C; U-100% 15N] YgaP, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-100% 13C; U-100% 15N; U-80% 2H]1
0.5 mMentity-2[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 7.0 ambient 303 K
20 7.0 ambient 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
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler 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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