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- PDB-1te7: Solution NMR Structure of Protein yqfB from Escherichia coli. Nor... -

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Basic information

Entry
Database: PDB / ID: 1te7
TitleSolution NMR Structure of Protein yqfB from Escherichia coli. Northeast Structural Genomics Consortium Target ET99
ComponentsHypothetical UPF0267 protein yqfB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA + BETA / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


N4-acetylcytidine amidohydrolase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / cytosol
Similarity search - Function
N(4)-acetylcytidine amidohydrolase / Hypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
N(4)-acetylcytidine amidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics with DYANA
AuthorsAtreya, H.S. / Shen, Y. / Yee, A. / Arrowsmith, C. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: G-Matrix Fourier Transform NOESY-Based Protocol for High-Quality Protein Structure Determination
Authors: Shen, Y. / Atreya, H.S. / Liu, G. / Szyperski, T.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 2, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Hypothetical UPF0267 protein yqfB


Theoretical massNumber of molelcules
Total (without water)11,9181
Polymers11,9181
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 least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein Hypothetical UPF0267 protein yqfB


Mass: 11918.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YQFB / Production host: Escherichia coli (E. coli) / References: UniProt: P67603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (5,2)D HACACONHN
141GFT (4,3)D (H)CCH COSY
1513D 15N,13Caliphatic,13Caromatic-resolved [1H,1H]-NOESY

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Sample preparation

DetailsContents: 1mM U-13C,15N YqfB,25 mM Na phosphate, 400 mM NaCl, 1 mM DTT, 20 mM ZnCl2, 0.01% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Temperature units: K

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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
PROSA6Guentertprocessing
XEASY1Bartels, Cdata analysis
AutoAssign1Moseley, H.N.M.data analysis
DYANA5Guentert, P.refinement
RefinementMethod: torsion angle dynamics with DYANA / Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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