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- PDB-2jso: Antimicrobial resistance protein -

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Basic information

Entry
Database: PDB / ID: 2jso
TitleAntimicrobial resistance protein
ComponentsPolymyxin resistance protein pmrD
KeywordsSIGNALING PROTEIN / protein / Antibiotic resistance / TRANSCRIPTION
Function / homologySignal transduction protein PmrD / Polymyxin resistance protein PmrD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #650 / Signal transduction protein PmrD superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / response to antibiotic / Beta Barrel / Mainly Beta / Signal transduction protein PmrD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsJin, C. / Fu, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: First structure of the polymyxin resistance proteins.
Authors: Fu, W. / Yang, F. / Kang, X. / Zhang, X. / Li, Y. / Xia, B. / Jin, C.
History
DepositionJul 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymyxin resistance protein pmrD


Theoretical massNumber of molelcules
Total (without water)9,8861
Polymers9,8861
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 Polymyxin resistance protein pmrD / BasR/pmrA posttranscriptional activator / Signal transduction protein pmrD


Mass: 9885.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pmrD / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P37590

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D HN(CO)CA
1923D (H)CCH-TOCSY
11023D HNHA
11123D 1H-15N NOESY
11223D 1H-13C NOESY
11323D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N], antimicrobial resistance protein, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N], antimicrobial resistance protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMantimicrobial resistance protein[U-100% 15N]1
1 mMantimicrobial resistance protein[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 80 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
RefinementMethod: simulated annealing / 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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