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- PDB-1q3t: Solution structure and function of an essential CMP kinase of Str... -

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Basic information

Entry
Database: PDB / ID: 1q3t
TitleSolution structure and function of an essential CMP kinase of Streptococcus pneumoniae
ComponentsCytidylate kinase
KeywordsTRANSFERASE / nucleotide monophosphate kinase / CMP kinase / cytidylate kinase
Function / homology
Function and homology information


(d)CMP kinase / cytidylate kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, L. / Mack, J. / Hajduk, P.J. / Kakavas, S.J. / Saiki, A.Y. / Lerner, C.G. / Olejniczak, E.T.
CitationJournal: Protein Sci. / Year: 2003
Title: Solution structure and function of an essential CMP kinase of Streptococcus pneumoniae
Authors: Yu, L. / Mack, J. / Hajduk, P.J. / Kakavas, S.J. / Saiki, A.Y. / Lerner, C.G. / Olejniczak, E.T.
History
DepositionJul 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidylate kinase


Theoretical massNumber of molelcules
Total (without water)26,3081
Polymers26,3081
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)1 / 20MINIMZED AVERAGE STRUCTURE
RepresentativeModel #1

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Components

#1: Protein Cytidylate kinase / / CK / Cytidine monophosphate kinase / CMP kinase


Mass: 26307.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: cmp / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97PK6, UMP/CMP kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D TRIPLE RESONANCE EXPERIMENTS
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 1MM CMP KINASE
Sample conditionsIonic strength: 20mM SODIUM PHOSPHATE, 50mM AmMONIUM SULFATE
pH: 7.0 / Pressure: AMBIENT / Temperature: 303 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
CNX2000BRUNGERrefinement
CNX2000structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: MINIMZED AVERAGE STRUCTURE / Conformers calculated total number: 20 / Conformers submitted total number: 1

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