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- PDB-1zts: Solution Structure of Bacillus Subtilis Protein YQBG: Northeast S... -

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Basic information

Entry
Database: PDB / ID: 1zts
TitleSolution Structure of Bacillus Subtilis Protein YQBG: Northeast Structural Genomics Consortium Target SR215
ComponentsHypothetical protein yqbG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA / GFT NMR / PROTEIN STRUCTURE INITIATIVE / PSI / NESG / SR215 / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / CYANA2.0
Function / homologyYqbG-like / Protein of unknown function DUF3199, YqbG / YqbG-like superfamily / Protein of unknown function (DUF3199) / Hypothetical protein yqbg / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YqbG
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS distance geometry
AuthorsLiu, G. / Shen, Y. / Xiao, R. / Acton, T. / Ma, L. / Joachimiak, A. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2006
Title: NMR structure of protein yqbG from Bacillus subtilis reveals a novel alpha-helical protein fold.
Authors: Liu, G. / Shen, Y. / Xiao, R. / Acton, T. / Ma, L.C. / Joachimiak, A. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Hypothetical protein yqbG


Theoretical massNumber of molelcules
Total (without water)15,7741
Polymers15,7741
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Hypothetical protein yqbG


Mass: 15773.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqbG / Plasmid: pSR215-21.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: P45923

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H] NOESY
121GFT (4,3)D HNNCABCB
131GFT (4,3)D CABCB(CO)NHN
141GFT (4,3)D HABCAB(CO)NHN
151GFT (4,3)D (H)CCH
NMR detailsText: by using CYANA2.0

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Sample preparation

DetailsContents: 0.94 MM, U-15N,13C; NMR BUFFER 6.5, 5% D2O, 0.02% NAN3, 10MM DTT, 5MM CACL2, 100MM NACL, 20MM MES,PH 6.5; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2P.GUNTERT ET AL.refinement
CYANA2P.GUNTERT ET AL.structure solution
XEASY1.3.1.3C. Bartels ET AL.data analysis
NMRPipe2.3G. Cornilescu ET ALprocessing
AutoStructure2.0.0Y J HUANG ET ALdata analysis
CYANA1.0.5P.GUNTERT ET AL.data analysis
RefinementMethod: TORSION ANGLE DYNAMICS distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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