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- PDB-2l8y: Solution structure of the E. coli outer membrane protein RcsF (pe... -

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Basic information

Entry
Database: PDB / ID: 2l8y
TitleSolution structure of the E. coli outer membrane protein RcsF (periplasmatic domain)
ComponentsProtein rcsF
KeywordsSIGNALING PROTEIN / two component system / RcsF / rcs signalling system / disulphide bridges / exopolysaccharide biosynthesis
Function / homology
Function and homology information


positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / cellular response to cell envelope stress / cell outer membrane / outer membrane-bounded periplasmic space / intracellular signal transduction
Similarity search - Function
Outer membrane lipoprotein RcsF / RcsF lipoprotein / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane lipoprotein RcsF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average
AuthorsRogov, V.V. / Rogova, N.Y. / Bernhard, F. / Lohr, F. / Doetsch, V.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A disulfide bridge network within the soluble periplasmic domain determines structure and function of the outer membrane protein RCSF.
Authors: Rogov, V.V. / Rogova, N.Y. / Bernhard, F. / Lohr, F. / Dotsch, V.
History
DepositionJan 27, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: 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_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein rcsF


Theoretical massNumber of molelcules
Total (without water)11,1371
Polymers11,1371
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)25 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein rcsF


Mass: 11136.781 Da / Num. of mol.: 1 / Fragment: periplasmatic domain, Residues 31-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rcsF / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 express / References: UniProt: P69411

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of periplasmatic domain of the E. coli outer membrane protein RcsF (residues 30-134)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNCO
1613D (HCA)CO(CA)NH
1713D H(CC)(CO)NH-TOCSY
1813D (H)CC(CO)NH-TOCSY
1913D 1H-13C NOESY aliphatic
11012D 1H-13C NOESY aromatic
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.6mM [U-98% 13C; U-98% 15N] RcsF(31-134); 50mM sodium phosphate; 100mM sodium chloride; 4.6mM protease inhibitors cocktail; 0.3mM DSS; 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRcsF(31-134)-1[U-98% 13C; U-98% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
4.6 mMprotease inhibitors cocktail-41
0.3 mMDSS-51
Sample conditionsIonic strength: 0.100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
Sparky112Goddarddata analysis
CYANA1.0.5Guntert, Mumenthaler and Wuthrichstructure solution
ARIA1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1195 / NOE intraresidue total count: 194 / NOE long range total count: 582 / NOE medium range total count: 225 / NOE sequential total count: 282 / Disulfide bond constraints total count: 12 / Hydrogen bond constraints total count: 88 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25 / Representative conformer: 23
NMR ensemble rmsDistance rms dev: 0.0138 Å / Distance rms dev error: 0.0009 Å

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