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- PDB-1z5f: Solution Structure of the Cytotoxic RC-RNase 3 with a Pyroglutama... -

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Basic information

Entry
Database: PDB / ID: 1z5f
TitleSolution Structure of the Cytotoxic RC-RNase 3 with a Pyroglutamate Residue at the N-terminus
ComponentsRC-RNase 3
KeywordsHYDROLASE / ribonuclease / pyroglutamate / cytotoxicity / bullfrog
Function / homology
Function and homology information


endonuclease activity / nucleic acid 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
: / RC-RNase3 ribonuclease
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodSOLUTION NMR / simulated annealing
AuthorsLou, Y.C. / Huang, Y.C. / Pan, Y.R. / Chen, C. / Liao, Y.D.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Roles of N-terminal pyroglutamate in maintaining structural integrity and pKa values of catalytic histidine residues in bullfrog ribonuclease 3
Authors: Lou, Y.C. / Huang, Y.C. / Pan, Y.R. / Chen, C. / Liao, Y.D.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Solution Structure of the Cytotoxic RNase 4 from OOcytes of Bullfrog Rana catesbeiana
Authors: Hsu, C.H. / Liao, Y.D. / Chen, L.W. / Wu, S.H. / Leu, Y.J. / Chen, C.
History
DepositionMar 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RC-RNase 3


Theoretical massNumber of molelcules
Total (without water)11,8951
Polymers11,8951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RC-RNase 3 / RC-RNase3 ribonuclease


Mass: 11894.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): Oocyte / References: GenBank: 15111749, UniProt: Q9DFY7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
132IPAP 1H, 15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM RC-RNase 3, U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22mM RC-RNase 3, U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O90% H2O, 10% D2O, 5mg/ml phage pf1
Sample conditionsIonic strength: 20 mM / pH: 3.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
NMRPipeprocessing
NMRView5data analysis
X-PLOR3.851structure solution
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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