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- PDB-1qwq: Solution structure of the monomeric N67D mutant of Bovine Seminal... -

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Basic information

Entry
Database: PDB / ID: 1qwq
TitleSolution structure of the monomeric N67D mutant of Bovine Seminal Ribonuclease
ComponentsRibonuclease
KeywordsHYDROLASE / ALPHA-BETA-PROTEIN
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / metabolic process / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
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
Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION
AuthorsAvitabile, F. / Alfano, C. / Spadaccini, R. / Crescenzi, O. / D'Ursi, A.M. / D'Alessio, G. / Tancredi, T. / Picone, D.
Citation
Journal: Biochemistry / Year: 2003
Title: THE SWAPPING OF TERMINAL ARMS IN RIBONUCLEASES: COMPARISON OF THE SOLUTION STRUCTURE OF MONOMERIC BOVINE SEMINAL AND PANCREATIC RIBONUCLEASES
Authors: Avitabile, F. / Alfano, C. / Spadaccini, R. / Crescenzi, O. / D'Ursi, A.M. / D'Alessio, G. / Tancredi, T. / Picone, D.
#1: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H and 15N sequential assignment and secondary structure of the monomeric N67D mutant of bovine seminal ribonuclease.
Authors: Crescenzi, O. / Carotenuto, A. / D'Ursi, A.M. / Tancredi, T. / D'Alessio, G. / Avitabile, F. / Picone, D.
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 16, 2003ID: 1O0G
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)13,6341
Polymers13,6341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease / / Seminal Ribonuclease


Mass: 13633.624 Da / Num. of mol.: 1 / Mutation: N67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SRN / Plasmid: PET-22B+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00669, EC: 3.1.27.5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
131HNHA
141HNHB
1522D NOESY
1622D TOCSY
1722D COSY
1822D NHSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0MM MONOMERIC BOVINE SEMINAL RIBONUCLEASE U-97% 15N95% H2O/5% D2O
22.0MM MONOMERIC BOVINE SEMINAL RIBONUCLEASE95% H2O/5% D2O
Sample conditionsIonic strength: 0 / pH: 5.65 / Pressure: ambient / Temperature: 300 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX4003

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
NMRView4.0.3data analysis
DYANA1.5structure solution
Amber6refinement
RefinementMethod: TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 16

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