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- PDB-1c54: SOLUTION STRUCTURE OF RIBONUCLEASE SA -

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Basic information

Entry
Database: PDB / ID: 1c54
TitleSOLUTION STRUCTURE OF RIBONUCLEASE SA
ComponentsRIBONUCLEASE SA
KeywordsHYDROLASE / ALPHA+BETA PROTEIN
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLaurents, D.V. / Canadillas-Perez, J.M. / Santoro, J. / Schell, D. / Pace, C.N. / Rico, M. / Bruix, M.
Citation
Journal: Proteins / Year: 2001
Title: Solution structure and dynamics of ribonuclease Sa.
Authors: Laurents, D. / Perez-Canadillas, J.M. / Santoro, J. / Rico, M. / Schell, D. / Pace, C.N. / Bruix, M.
#1: Journal: J.Biomol.NMR / Year: 1999
Title: Sequential Assignment and Solution Secondary Structure of Doubly Labelled Ribonuclease Sa
Authors: Laurents, D.V. / Canadillas-Perez, J.M. / Santoro, J. / Schell, D. / Pace, C.N. / Rico, M. / Bruix, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Ribonucelase from Streptomyces Aureofaciens at Atomic Resolution
Authors: Sevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
History
DepositionOct 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 9, 2024Group: Structure summary / Category: 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 SA


Theoretical massNumber of molelcules
Total (without water)10,5821
Polymers10,5821
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 / 40LOWEST ENERGY AND REPRESENTATIVE OF DIFFERENT CONFORMERS
RepresentativeModel #1lowest energy

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Components

#1: Protein RIBONUCLEASE SA


Mass: 10582.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Plasmid: PEH100 / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3
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
NMR detailsText: THIS STRUCTURE WAS DETERMINED WITH A 80MS MIXING TIME, AND STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
1NA
2NA
3U-15N
4U-15N
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
105.5AMBIENT 303.2 K
205.5AMBIENT 303.2 K
305.5AMBIENT 303.2 K
405.5AMBIENT 303.2 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
XwinNMR1.3BRUKERaquisition
ANSIG3.3KRAULISprocessing
DYANA1.4GUNTERstructure solution
GROMOSVAN GUNSTRUMrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1924 UPPER DISTANCE RESTRAINTS, DERIVED FROM 2276 UNAMBIGUOUS NOES, AND 3 LOWER DISTANCE RESTRAINTS BASED ON THE PROTEINS C7-C96 DISULFIDE BOND.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY AND REPRESENTATIVE OF DIFFERENT CONFORMERS
Conformers calculated total number: 40 / Conformers submitted total number: 20

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