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- PDB-2g7j: Solution NMR structure of the putative cytoplasmic protein ygaC f... -

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Basic information

Entry
Database: PDB / ID: 2g7j
TitleSolution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72.
Componentsputative cytoplasmic proteinCytoplasm
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / StR72 / AUTOSTRUCTURE / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF2002 / Protein of unknown function DUF2002 / Protein of unknown function (DUF2002) / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / : / Putative cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. ...Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72.
Authors: Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)14,4051
Polymers14,4051
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein putative cytoplasmic protein / Cytoplasm


Mass: 14405.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ygaC / Plasmid: StR72-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: GenBank: 16421350, UniProt: Q8ZML5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1324D 13C-separated NOESY
141HNHA
153high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls)
161backbone TR expts
1723D (H)CCH-COSY
1813D TOCSYs, aromatic expts
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 to 112, PSVS 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3-43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, 0.846.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5, 5% D2O/95% H2O5% D2O/95% H2O
21.12mM U-13C,15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5, 100% D2O100% D2O
31.07mM 5%-13C,U-15N StR72, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, pH 6.5, 5% D2O/95% H2O5% D2O/95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5pl6Brukercollection
VNMR6.1CVariancollection
Sparky3.11Goddard & Knellerdata analysis
AutoAssign1.17.0Zimmerman, Moseley, Montelionedata analysis
AutoStructure2.1.1Huang & Montelionerefinement
XPLOR-NIH2.11.2Clore et al.refinement
CNS1.1Brunger et al.refinement
PdbStat4.01Tejero & Montelionedata analysis
PSVS1.2Bhattacharya & Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS PER RESIDUE, 6.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 to 112 BY PSVS 1.2). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED C-TERMINUS OF THE PROTEIN (EKTD + LEHHHHHH TAG) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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