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- PDB-1tm9: NMR Structure of gene target number gi3844938 from Mycoplasma gen... -

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Basic information

Entry
Database: PDB / ID: 1tm9
TitleNMR Structure of gene target number gi3844938 from Mycoplasma genitalium: Berkeley Structural Genomics Center
ComponentsHypothetical protein MG354
KeywordsStructural genomics / unknown function / all alpha helical protein / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologyHypothetical protein MG354 fold / MG354-like / Protein of unknown function DUF1951 / MG354-like superfamily / Domain of unknown function (DUF1951) / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein MG354
Function and homology information
Biological speciesMycoplasma genitalium (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPelton, J.G. / Shi, J. / Yokota, H. / Kim, R. / Wemmer, D.E. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: To be Published
Title: NMR Structure of Gene Target gi3844938 from Mycoplasma genitalium
Authors: Pelton, J.G. / Shi, J. / Yokota, H. / Kim, R. / Wemmer, D.E.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MG354


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
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)26 / 200structures with favorable non-bond energy, structures with the least restraint violations, target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Hypothetical protein MG354 / gi3844938


Mass: 15717.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Gene: MG354 / Plasmid: pSJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1214D 13C-separated NOESY
1314D 13C/15N-separated NOESY
141HNHA
1513D 15N-separated NOESY
1612D NOESY
NMR detailsText: NOEs to PHE sidechains were identified in 2D 13C half-filtered and 2D 13C double half-filtered NOESY spectra on a sample with unlabeled PHE and all other residues both 15N and 13C labeled

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Sample preparation

DetailsContents: 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM EDTA, 1 mM TCEP
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.14 / pH: 6.7 / 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
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
NMRPipe2.1processing
NMRView5.0.4data analysis
XwinNMR3.1collection
DYANA1.5refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on 850 NOE restraints (278 intra-residue, 238 sequential, 213 medium-range, and 121 long-range), 86 hydrogen bond restraints (43 hydrogen bonds), and 69 PHI torsion ...Details: Structures are based on 850 NOE restraints (278 intra-residue, 238 sequential, 213 medium-range, and 121 long-range), 86 hydrogen bond restraints (43 hydrogen bonds), and 69 PHI torsion angle restraints, using the program DYANA. The structures were not energy minimized.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, structures with the least restraint violations, target function
Conformers calculated total number: 200 / Conformers submitted total number: 26

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