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- PDB-2kb6: Solution structure of onconase C87A/C104A -

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Basic information

Entry
Database: PDB / ID: 2kb6
TitleSolution structure of onconase C87A/C104A
ComponentsProtein P-30
KeywordsHYDROLASE / protein / RNase / Endonuclease / Nuclease / Pyrrolidone carboxylic acid
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
AuthorsWeininger, U. / Schulenburg, C. / Arnold, U. / Ulbrich-Hofmann, R. / Balbach, J.
CitationJournal: Chembiochem / Year: 2010
Title: Impact of the C-terminal disulfide bond on the folding and stability of onconase.
Authors: Schulenburg, C. / Weininger, U. / Neumann, P. / Meiselbach, H. / Stubbs, M.T. / Sticht, H. / Balbach, J. / Ulbrich-Hofmann, R. / Arnold, U.
History
DepositionNov 21, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence
Category: entity_poly / pdbx_nmr_sample_details ...entity_poly / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_sample_details.contents ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 30, 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: Protein P-30


Theoretical massNumber of molelcules
Total (without water)11,7821
Polymers11,7821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein P-30 / Onconase


Mass: 11781.518 Da / Num. of mol.: 1 / Mutation: C87A, C104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / 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
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-15N] Onconase, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Onconase / Isotopic labeling: [U-15N]
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue, Nilgesstructure solution
ARIALinge, O'Donoghue, Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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