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- PDB-1r4y: SOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTO... -

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Entry
Database: PDB / ID: 1r4y
TitleSOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN
ComponentsRibonuclease alpha-sarcin
KeywordsHYDROLASE / ALPHA-BETA PROTEIN
Function / homology
Function and homology information


ribotoxin / rRNA endonuclease activity / negative regulation of cytoplasmic translation / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Fungal ribotoxin / : / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease alpha-sarcin
Similarity search - Component
Biological speciesAspergillus giganteus (mold)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGarcia-Mayoral, M.F. / Garcia-Ortega, L. / Lillo, M.P. / Santoro, J. / Martinez Del Pozo, A. / Gavilanes, J.G. / Rico, M. / Bruix, M.
Citation
Journal: Protein Sci. / Year: 2004
Title: NMR structure of the noncytotoxic {alpha}-sarcin mutant {Delta}(7-22): The importance of the native conformation of peripheral loops for activity.
Authors: Garcia-Mayoral, M.F. / Garcia-Ortega, L. / Lillo, M.P. / Santoro, J. / Martinez Del Pozo, A. / Gavilanes, J.G. / Rico, M. / Bruix, M.
#1: Journal: Biochemistry / Year: 1998
Title: Characterization of pKa values and titration shifts in the cytotoxic ribonuclease alpha-sarcin by NMR. Relationship between electrostatic interactions, structure, and catalytic function.
Authors: Perez-Canadillas, J.M. / Campos-Olivas, R. / Lacadena, J. / Martinez del Pozo, A. / Gavilanes, J.G. / Santoro, J. / Rico, M. / Bruix, M.
#2: Journal: FEBS Lett. / Year: 1996
Title: Structural basis for the catalytic mechanism and substrate specificity of the ribonuclease alpha-sarcin.
Authors: Campos-Olivas, R. / Bruix, M. / Santoro, J. / Martinez del Pozo, A. / Lacadena, J. / Gavilanes, J.G. / Rico, M.
#3: Journal: J.Mol.Biol. / Year: 2000
Title: The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity.
Authors: Perez-Canadillas, J.M. / Santoro, J. / Campos-Olivas, R. / Lacadena, J. / Martinez del Pozo, A. / Gavilanes, J.G. / Rico, M. / Bruix, M.
#4: Journal: To be Published
Title: Dissecting structural and electrostatic interactions of charged groups in alpha-sarcin. An NMR study of some mutants involving the catalytic residues.
Authors: Garcia-Mayoral, M.F. / Perez-Canadillas, J.M. / Santoro, J. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. / Lacadena, J. / Martinez del Pozo, A. / Gavilanes, J.G. / Rico, M. / Bruix, M.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 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: Ribonuclease alpha-sarcin


Theoretical massNumber of molelcules
Total (without water)15,1631
Polymers15,1631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease alpha-sarcin / rRNA endonuclease


Mass: 15162.897 Da / Num. of mol.: 1 / Mutation: L7G, R22G, DEL(8-21)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus giganteus (mold) / Gene: SAR / Plasmid: pINPGOmpAaSD(7-22) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00655, EC: 3.1.27.10
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1322D NOESY
1422D TOCSY
NMR detailsText: This structure was determined using standard 2D NOE homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Ribonuclease; 90% H2O, 10% D2O90% H2O/10% D2O
22mM Ribonuclease; D2OD2O
Sample conditionspH: 6 / Pressure: AMBIENT / Temperature: 308 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1collection
XwinNMR3.1processing
ANSIG3.3Kraulis, P.data analysis
DYANA1.5Guntert, P.structure solution
DYANA1.5Guntert, P.refinement
Amber7refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 2088 restraints, 1990 NOE-derived distance constraints and 98 dihedral angle restraints. The best 25 representative conformers are energy-minimized with AMBER7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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