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- PDB-2lqv: YebF -

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Basic information

Entry
Database: PDB / ID: 2lqv
TitleYebF
ComponentsProtein yebF
KeywordsPROTEIN TRANSPORT / secretion
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Uncharacterised protein family YebF / YebF/Colicin-M immunity protein / YebF/Colicin-M immunity protein / YebF/Cmi superfamily / YebF-like protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailsclosest to the average, model 1
AuthorsPrehna, G. / Zhang, G. / Gong, X. / Duszyk, M. / Okon, M. / Mcintosh, L.P. / Weiner, J.H. / Strynadka, N.C.J.
CitationJournal: Structure / Year: 2012
Title: A Protein Export Pathway Involving Escherichia coli Porins.
Authors: Prehna, G. / Zhang, G. / Gong, X. / Duszyk, M. / Okon, M. / McIntosh, L.P. / Weiner, J.H. / Strynadka, N.C.
History
DepositionMar 16, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein yebF


Theoretical massNumber of molelcules
Total (without water)11,8831
Polymers11,8831
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 / 10target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein yebF


Mass: 11883.173 Da / Num. of mol.: 1 / Fragment: UNP residues 22-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yebF, b1847, JW1836 / Production host: Escherichia coli (E. coli) / References: UniProt: P33219

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
191CCC-TOCSY-NNH
1101HCC-TOCSY-NNH
1111(HB)CB(CGCD)HD-aromatic
1121HBGCBGCCBGCACONNH
1131CT-HSQC
21412D 1H-15N HSQC
21513D CBCA(CO)NH
21613D HN(CA)CB
21713D HNCO
21813D HCACO
21913D (H)CCH-TOCSY
22013D 1H-15N NOESY
22113D 1H-13C NOESY
2221CCC-TOCSY-NNH
2231HCC-TOCSY-NNH
2241(HB)CB(CGCD)HD-aromatic
2251HBGCBGCCBGCACONNH
2261CT-HSQC

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Sample preparation

DetailsContents: 0.5-1 mM [U-100% 13C; U-100% 15N] E coli protein, 50 mM HEPES, 100 mM sodium chloride, 0.1 mM TCEP, 0.1 mM PMSF, 95 % H2O, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mME coli protein-1[U-100% 13C; U-100% 15N]0.5-11
50 mMHEPES-21
100 mMsodium chloride-31
0.1 mMTCEP-41
0.1 mMPMSF-51
95 %H2O-61
5 %D2O-71
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.5 ambient 298 K
20.1 6.5 ambient 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian UnityVarianUNITY6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawJohnson, One Moon Scientificdata analysis
NMRDrawJohnson, One Moon Scientificprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10 / Conformers submitted total number: 10

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