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- PDB-1ywl: Solution NMR structure of the protein EF2693 from E. faecalis: No... -

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Basic information

Entry
Database: PDB / ID: 1ywl
TitleSolution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36
ComponentsHypothetical UPF0213 protein EF2693
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha and beta / Northeast Structural Genomics Consortium (NESG) / Protein Structure Initiative (PSI)
Function / homologyGIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / 3-Layer(aba) Sandwich / Alpha Beta / UPF0213 protein EF_2693
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsNortheast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36
Authors: Swapna, G.V.T. / Bhattacharya, A. / Aramini, J.M. / Acton, T.B. / Ma, L. / Xiao, R. / Shastry, R. / Shih, L. / Cunningham, K.E. / Montelione, G.T.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 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_nmr_spectrometer / 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 / _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: Hypothetical UPF0213 protein EF2693


Theoretical massNumber of molelcules
Total (without water)11,5021
Polymers11,5021
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 / 56Structures with lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical UPF0213 protein EF2693


Mass: 11502.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF2693 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q830S9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Automatic backbone resonance assignments were made using AutoAssign. Side-chain assignments were made manually. Automatic ...Text: The structure was determined using triple-resonance NMR spectroscopy. Automatic backbone resonance assignments were made using AutoAssign. Side-chain assignments were made manually. Automatic NOE assignments were made using AutoStructure. Dihedral angle restraints were made using Hyper and Talos. The SPINS database software was used as an integrating agent. PSVS was used to validate structure quality.

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Sample preparation

DetailsContents: 5% D2O, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 5 % D20, 95 % H20
Solvent system: 5 % D20, 95 % H20
Sample conditionsIonic strength: 100 mM NaCl, 5 mM CaCl2 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 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 AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, et alrefinement
AutoStructure2.0.0Huangstructure solution
AutoAssign1.14Moseley, et aldata analysis
NMRPipe2.1Delaglio, et alprocessing
VNMR6.1BVariancollection
XwinNMR3.5Brukercollection
PdbStat4.01Tejero and Montelionestructure solution
HYPER3.2Tejero and Montelionestructure solution
TALOS2.1Cornilescu, et alstructure solution
SPINS5Barandata analysis
PSVS1Bhattacharyarefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 912 conformationally-restricting noe-derived distance restraints, 216 dihedral restraints and 54 hydrogen bond restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Structures with lowest energy / Conformers calculated total number: 56 / Conformers submitted total number: 10

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