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- PDB-1ovq: Solution structure of the hypothetical protein YqgF from Escheric... -

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Basic information

Entry
Database: PDB / ID: 1ovq
TitleSolution structure of the hypothetical protein YqgF from Escherichia coli
ComponentsHypothetical protein yqgFHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-alpha
Function / homology
Function and homology information


rRNA 5'-end processing / 3'-5'-DNA exonuclease activity / ribosome biogenesis / Hydrolases; Acting on ester bonds / cytoplasm
Similarity search - Function
Putative pre-16S rRNA nuclease / Holliday junction resolvase / YqgF/RNase H-like domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / YqgF/RNase H-like domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative pre-16S rRNA nuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, D. / Wang, Y.S. / Wyss, D.F.
CitationJournal: J.Biomol.NMR / Year: 2003
Title: Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold.
Authors: Liu, D. / Wang, Y.S. / Wyss, D.F.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yqgF


Theoretical massNumber of molelcules
Total (without water)15,2051
Polymers15,2051
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)25 / 100back calculated data agree with experimental NOESY spectrum
Representative

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Components

#1: Protein Hypothetical protein yqgF / Hypothesis


Mass: 15205.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YQGF OR B2949 OR C3535 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A8I1

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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
1323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N,13C; 75 mM KiPO4, pH 7.5, 5 mM DTT95% H2O/5% D2O
2U-15N,13C; 75 mM KiPO4, pH 7.5, 5 mM DTT99%D2O
Sample conditionsIonic strength: 0.45 / pH: 7.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR98msistructure solution
Felix98msiprocessing
X-PLOR98msirefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 25

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