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- PDB-1pu3: The Solution NMR Structure and Dynamics of a Recombinant Onconase... -

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Basic information

Entry
Database: PDB / ID: 1pu3
TitleThe Solution NMR Structure and Dynamics of a Recombinant Onconase with Altered N-terminal and Met23 residues
ComponentsP-30 protein
KeywordsHYDROLASE / bowl-shaped folding of the two sheets
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesRana pipiens (northern leopard frog)
MethodSOLUTION NMR / simulated annealing, matrix relaxation, torsion angle dymanics
Model type detailsminimized average
AuthorsGorbatyuk, V.Y. / Tsai, C.K. / Chang, C.F. / Huang, T.H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Effect of N-terminal and Met23 Mutations on the Structure and Dynamics of Onconase
Authors: Gorbatyuk, V.Y. / Tsai, C.K. / Chang, C.F. / Huang, T.H.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-30 protein


Theoretical massNumber of molelcules
Total (without water)11,9761
Polymers11,9761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein P-30 protein / Onconase


Mass: 11975.836 Da / Num. of mol.: 1 / Mutation: M23L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Plasmid: pET-11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22069, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
1313D 13C-separated NOESY
1412D TOCSY
1512D NOESY

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Sample preparation

DetailsContents: 1.5 mM (M-1, Q1, M23L)rONC [U-15N; U-13C]
Solvent system: 50mM phosphate buffer pH4.1, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0.3 / pH: 4.1 / Pressure: ambient / Temperature: 310 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: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Nilgesstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing, matrix relaxation, torsion angle dymanics
Software ordinal: 1
Details: the structures are based on a total of 1802 restraints, 1550 are NOE-derived distance constraints, 4 disulfide bonds, 150 dihedral angle restraints, 98 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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