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- PDB-1n91: Solution NMR Structure of Protein yggU from Escherichia coli. Nor... -

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Basic information

Entry
Database: PDB / ID: 1n91
TitleSolution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14.
Componentsorf, hypothetical protein
KeywordsStructural Genomics/Unknown function / ALPHA+BETA / Northeast Structural Genomics Consortium / PSI / Protein Structure Initiative / NESG / Structural Genomics-Unknown function COMPLEX
Function / homologyConserved Hypothetical Protein Mth637; Chain: A; / YggU-like / Protein of unknown function DUF167 / YggU-like superfamily / Uncharacterised ACR, YggU family COG1872 / DUF167 / 2-Layer Sandwich / Alpha Beta / UPF0235 protein YggU
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsAramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biomol.Nmr / Year: 2003
Title: Resonance assignments for the hypothetical protein yggU from Escherichia coli.
Authors: Aramini, J.M. / Mills, J.L. / Xiao, R. / Acton, T.B. / Wu, M.J. / Szyperski, T. / Montelione, G.T.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 650HELIX Author defined secondary structure.
Remark 700SHEET The sheet structure of this molecule is bifurcated. In order to represent this feature in the ...SHEET The sheet structure of this molecule is bifurcated. In order to represent this feature in the sheet report below, two sheets are defined. Strands 1,2 and 3 in sheet A and B are identical.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: orf, hypothetical protein


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein orf, hypothetical protein


Mass: 11903.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: yggU / Plasmid: ER14-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pMgk / References: UniProt: Q8XCU6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-NOESY
1213D 13C-NOESY
1313D aromatic 13C-NOESY
1422D 15N,1H HSQC-J
1512D 15N,1H MEXICO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Automatic backbone resonance assignments were made using AUTOASSIGN. Automatic NOESY assignments as well as distance and ...Text: The structure was determined using triple-resonance NMR spectroscopy. Automatic backbone resonance assignments were made using AUTOASSIGN. Automatic NOESY assignments as well as distance and hydrogen bond restraints were determined using the AUTOSTRUCTURE program. Dihedral angle restraints were determined using HYPER and TALOS. Backbone conformations for residues 1-5, 25-26, 66, 101-108 are not well-defined [S(phi) + S(psi) < 1.8] in this solution NMR structure.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM ER14 U-15N,13C in 20mM MES, 50mM NaCl, 5mM DTT, pH 6.595% H2O/5% D2O
21.0 mM ER14 U-15N,13C in 20mM MES, 50mM NaCl, 5mM DTT, pH 6.595% H2O/5% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVARIAN Inc.collection
NMRPipe2.1Delaglio, Baxprocessing
Sparky3.106Goddard, Knellerdata analysis
AutoAssign1.9Moseley, Zimmerman, Montelionedata analysis
AutoStructure1.1.2Huang, Montelionestructure solution
HYPER2.7Tejero, Montelionestructure solution
TALOS2.1Cornilescu, Delaglio, Baxstructure solution
DYANA1.5Guntertrefinement
X-PLOR2.0.4 (NIH)Brungerrefinement
PdbStat3.27Tejero, Montelionedata analysis
AutoStructure1.1.2Huangrefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1419 conformationally-restricting NOE-derived distance restraints, 210 dihedral angle restraints, and 78 hydrogen bond restraints. Initial structure ...Details: The structures are based on a total of 1419 conformationally-restricting NOE-derived distance restraints, 210 dihedral angle restraints, and 78 hydrogen bond restraints. Initial structure determination was performed by torsion angle dynamics (DYANA). The final structures submitted were refined by simulated annealing (XPLOR).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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