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- PDB-1kvz: Solution Structure of Cytotoxic RC-RNase4 -

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Basic information

Entry
Database: PDB / ID: 1kvz
TitleSolution Structure of Cytotoxic RC-RNase4
ComponentsRC-RNase4
KeywordsHYDROLASE / antitumor / bullfrog / cytotoxicity / ribonuclease / Structure from MOLMOL
Function / homology
Function and homology information


P-30 Protein / Ribonuclease A-like domain / 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
RC-RNase4 ribonuclease
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodSOLUTION NMR / simulated annealing
AuthorsHsu, C.-H. / Liao, Y.-D. / Chen, L.-W. / Wu, S.-H. / Chen, C.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Solution Structure of the Cytotoxic RNase 4 from the Oocytes of Bullfrog Rana Catesbeiana
Authors: Hsu, C.-H. / Liao, Y.-D. / Pan, Y.-R. / Chen, L.-W. / Wu, S.-H. / Leu, Y.-J. / Chen, C.
History
DepositionJan 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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
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
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Oct 23, 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: RC-RNase4


Theoretical massNumber of molelcules
Total (without water)12,2361
Polymers12,2361
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)15 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RC-RNase4


Mass: 12236.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Gene: Oocytes / Plasmid: PET-11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9DFY6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
232HNHA
NMR detailsText: This structure was determined using standard 3D hetreonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM rRC-RNase4 U-15N, 13C; 50mM phosphate buffer; 90% H2O, 10%90% H2O/10% D2O
21.5mM rRC-RNase4 U-15N; 50mM phosphate buffer; 90% H2O, 10%90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.51 atm310 K
23.51 atm310 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 AVANCEBrukerAVANCE6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
AURELIA2.6Brukerdata analysis
X-PLOR98MSIstructure solution
X-PLOR98MSIrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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