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- PDB-2ilx: Solution structure of catalytic domain of rat 2',3'-cyclic-nucleo... -

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Basic information

Entry
Database: PDB / ID: 2ilx
TitleSolution structure of catalytic domain of rat 2',3'-cyclic-nucleotide 3'-phosphodiesterase (CNP) protein
Components2',3'-cyclic-nucleotide 3'-phosphodiesterase
KeywordsHYDROLASE / CNP / CNPase / nervous system
Function / homology
Function and homology information


cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial outer membrane / response to lipopolysaccharide / mitochondrial inner membrane / perinuclear region of cytoplasm / RNA binding / extracellular space / membrane / cytoplasm
Similarity search - Function
2',3'-cyclic nucleotide 3'-phosphodiesterase fold / 2',3'-cyclic nucleotide 3'-phosphodiesterase superfamily / Cyclic nucleotide phosphodiesterase / : / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / AAA domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A.Y. / Kozlov, G. / Gehring, K.
CitationJournal: Febs J. / Year: 2007
Title: Solution structure of the catalytic domain of RICH protein from goldfish.
Authors: Kozlov, G. / Denisov, A.Y. / Pomerantseva, E. / Gravel, M. / Braun, P.E. / Gehring, K.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2007ID: 1N4T
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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 1.4May 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: 2',3'-cyclic-nucleotide 3'-phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)24,2521
Polymers24,2521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy and the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNP / CNPase


Mass: 24251.830 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P13233, 2',3'-cyclic-nucleotide 3'-phosphodiesterase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited NOESY
12113C-edited NOESY
131HN(CA)CB
141CBCA(CO)HN
151HNCO
162IPAP-HSQC
NMR detailsText: the structure was determined using multi-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM CNP U-15N, 13C; 50 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21 mM CNP U-15N; 50 mM MES buffer; 1% C12E5/hexanol; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.15 mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 310 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
Varian UNITYPLUSVarianUNITYPLUS8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2Delargio et al.processing
XEASY1.3.13Bartels et al.data analysis
CNS1.1Brunger et al.refinement
ARIA1.1Nilges et al.data analysis
TALOS2003Cornilescu et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structure was refined by using standard protocol in CNS with restraints from NOE distances, backbone torsion angles, hydrogen bonds and residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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