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- PDB-2k5t: Solution NMR Structure of Putative N-Acetyl Transferase YhhK from... -

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Basic information

Entry
Database: PDB / ID: 2k5t
TitleSolution NMR Structure of Putative N-Acetyl Transferase YhhK from E. coli Bound to Coenzyme A: Northeast Structural Genomics Consortium Target ET106
ComponentsUncharacterized protein yhhK
KeywordsTRANSFERASE / N-acetyl transferase / CoA / bound ligand / coenzyme A / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / unknown function
Function / homology
Function and homology information


acetyl-CoA binding / pantothenate biosynthetic process / zymogen activation / acyltransferase activity, transferring groups other than amino-acyl groups / protein processing
Similarity search - Function
PanD regulatory factor PanZ / PanZ, acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain, PanZ / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PanD regulatory factor
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsCort, J.R. / Yee, A. / Montelione, G.T. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Putative N-Acetyl Transferase YhhK from E. coli Bound to Coenzyme A
Authors: Cort, J.R. / Yee, A. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein yhhK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3782
Polymers14,6111
Non-polymers7681
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30fewest restraints violations and energies, favorable backbone geometry, minimal clashes
RepresentativeModel #1no criterion

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Components

#1: Protein Uncharacterized protein yhhK


Mass: 14610.599 Da / Num. of mol.: 1 / Mutation: A119T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: coli / Gene: yhhK, b3459, JW3424 / Plasmid: pET / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37613
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D (H)CCH-TOCSY
1713D (H)CCH-COSY
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11124D 13C HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 7 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
20.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 100 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMYhhK[U-100% 13C; U-100% 15N]1
5 mMCoenzyme A1
7 %D2O1
300 mMsodium chloride1
25 mMTRIS1
5 mMDTT1
0.6 mMYhhK[U-100% 13C; U-100% 15N]2
5 mMCoenzyme A2
100 %D2O2
300 mMsodium chloride2
25 mMTRIS2
5 mMDTT2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.data analysis
SparkyGoddardprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
AutoStructureHuang, Tejero, Powers and Montelionerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: no criterion
NMR ensembleConformer selection criteria: fewest restraints violations and energies, favorable backbone geometry, minimal clashes
Conformers calculated total number: 30 / Conformers submitted total number: 20

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