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- PDB-2k14: Solution structure of the soluble domain of the NfeD protein YuaF... -

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Basic information

Entry
Database: PDB / ID: 2k14
TitleSolution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis
ComponentsYuaF protein
KeywordsUNKNOWN FUNCTION / YuaF / Bacillus subtilis / NfeD-like protein / cellular stress
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / membrane raft / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / plasma membrane / Membrane protein NfeD2
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsThis PBD entry contains the structure of residues 97 to 174 of YuaF (residues 7 to 84 of this entry) ...This PBD entry contains the structure of residues 97 to 174 of YuaF (residues 7 to 84 of this entry). In addition, the structure includes six further residues (1-6) that originate from the MBP fusion construct.
AuthorsWalker, C.A. / Hinderhofer, M. / Witte, D.J. / Boos, W. / Moller, H.M.
CitationJournal: J.Biomol.Nmr / Year: 2008
Title: Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis.
Authors: Walker, C.A. / Hinderhofer, M. / Witte, D.J. / Boos, W. / Moller, H.M.
History
DepositionFeb 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YuaF protein


Theoretical massNumber of molelcules
Total (without water)8,8511
Polymers8,8511
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)20 / 400structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein YuaF protein


Mass: 8850.825 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 97-174)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Marburg 168
Description: The plasmid pHIHO1421 was constructed by fusing the coding sequence of residues 97-174 of YuaF to the 3'-end of the malE gene containing an additional thrombin cleavage site. The soluble ...Description: The plasmid pHIHO1421 was constructed by fusing the coding sequence of residues 97-174 of YuaF to the 3'-end of the malE gene containing an additional thrombin cleavage site. The soluble C-terminal domain of YuaF was generated by cleaving off the malE part by digestion with thrombin.
Gene: yuaF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O32077
Sequence detailsTHIS PBD ENTRY CONTAINS THE STRUCTURE OF RESIDUES 97 TO 174 OF YUAF (RESIDUES 7 TO 84 OF THIS ENTRY) ...THIS PBD ENTRY CONTAINS THE STRUCTURE OF RESIDUES 97 TO 174 OF YUAF (RESIDUES 7 TO 84 OF THIS ENTRY). IN ADDITION, THE STRUCTURE INCLUDES SIX FURTHER RESIDUES (1-6) THAT ORIGINATE FROM THE MBP FUSION CONSTRUCT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This PBD entry contains the structure of residues 97 to 174 of YuaF (residues 7 to 84 of this entry). In addition, the structure includes six further residues (1-6) that originate from the MBP fusion construct.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1613D HN(CA)CB
1733D 1H-15N TOCSY
1833D 1H-15N NOESY
1923D (H)CCH-COSY
11023D (H)CCH-TOCSY
11123D 1H-13C NOESY
1122(HB)CB(CGCD)HD
1132(HB)CB(CGCDCE)HE
11422D 1H-13C HSQC aromatic
11523D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.9 mM [U-13C; U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide, 100% D2O100% D2O
31 mM [U-15N] YuaF, 50 mM TRIS, 300 mM sodium chloride, 4 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMYuaF[U-13C; U-15N]1
50 mMTRIS1
300 mMsodium chloride1
4 mMsodium azide1
0.9 mMYuaF[U-13C; U-15N]2
50 mMTRIS2
300 mMsodium chloride2
4 mMsodium azide2
1 mMYuaF[U-15N]3
50 mMTRIS3
300 mMsodium chloride3
4 mMsodium azide3
Sample conditionsIonic strength: 300 / pH: 7.5 / Pressure: ambient atm / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance DRXBrukerAVANCE DRX6001
Bruker Avance IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
XwinNMR3.6Bruker Biospincollection
CARA1.8.4Keller and Wuthrichchemical shift assignment
TopSpin1.3.b.20Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: 400 Starting structures for refinement were generated with the final set of constraints by torsion angle dynamics in CYANA 2.0., Refinement of the final structural ensemble was carried out ...Details: 400 Starting structures for refinement were generated with the final set of constraints by torsion angle dynamics in CYANA 2.0., Refinement of the final structural ensemble was carried out by molecular dynamics simulated annealing in AMBER 8. The 100 structures with lowest target function in CYANA 2.0 were imported into AMBER 8, minimized and subjected to simulated annealing in vacuum with charges reduced to 20% of their original value. The final round of simulated annealing was carried out within a generalized-Born solvation model with full charges followed by energy minimization. Constraints from CYANA were translated into AMBER 8 format taking stereospecific assignments, pseudoatom corrections and NOE-averaging into account.
NMR constraintsNOE constraints total: 1526 / NOE intraresidue total count: 379 / NOE long range total count: 522 / NOE medium range total count: 214 / NOE sequential total count: 411
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.17 Å
NMR ensemble rmsDistance rms dev: 0.088 Å

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