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- PDB-1de3: SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN -

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Basic information

Entry
Database: PDB / ID: 1de3
TitleSOLUTION STRUCTURE 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
AuthorsPerez-Canadillas, J.M. / Campos-Olivas, R. / Santoro, J. / Lacadena, J. / Martinez del Pozo, A. / Gavilanes, J.G. / Rico, M. / Bruix, M.
Citation
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.
#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.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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)17,0131
Polymers17,0131
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)20 / 47structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RIBONUCLEASE ALPHA-SARCIN


Mass: 17012.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus giganteus (mold) / Strain: MDH 18894 / Plasmid: PINPGAS / Production host: Escherichia coli (E. coli) / 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
2222D NOESY
1311H-15N 3JHNHA MODULATED HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
1NA
2NA
3U-15N
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16AMBIENT 308 K
24AMBIENT 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1processing
ANSIG3.3KRAULISdata analysis
DYANA1.5GUNTERTstructure solution
GROMOS97VAN GUNSTERENstructure solution
GROMOS97VAN GUNSTERENrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2777 RESTRAINTS, 2658 ARE NOE-DERIVED DISTANCE CONSTRAINTS AND 119 DIHEDRAL PHI ANGLE RESTRAINTS. THE STRUCTURES WERE ENERGY MINIMISED WITH THE GROMOS FORCE FIELD.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 47 / Conformers submitted total number: 20

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