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- PDB-1bc4: THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYT... -

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Basic information

Entry
Database: PDB / ID: 1bc4
TitleTHE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES
ComponentsRIBONUCLEASE
KeywordsHYDROLASE / PHOSPHORIC DIESTER / RC-RNASE / CYTOTOXIC PROTEIN / SIALIC ACID BINDING LECTIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / carbohydrate binding / endonuclease activity / nucleic acid binding / extracellular region
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
Oocytes ribonuclease
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING
AuthorsChang, C.-F. / Chen, C. / Chen, Y.-C. / Hom, K. / Huang, R.-F. / Huang, T.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbeiana (bullfrog).
Authors: Chang, C.F. / Chen, C. / Chen, Y.C. / Hom, K. / Huang, R.F. / Huang, T.H.
#1: Journal: J.Biomol.NMR / Year: 1996
Title: The Secondary Structure of a Pyrimidine-Guanine Sequence-Specific Ribonuclease Possessing Cytotoxic Activity from the Oocytes of Rana Catesbeiana
Authors: Chen, C. / Hom, K. / Huang, R.F. / Chou, P.J. / Liao, Y.D. / Huang, T.
History
DepositionMay 5, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _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: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)12,4591
Polymers12,4591
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein RIBONUCLEASE / / RC RNASE


Mass: 12459.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rana catesbeiana (American bullfrog) / References: UniProt: P11916, 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
111DQF-COSY
121TOCSY
131NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TWO-DIMENSIONAL 1H NMR.

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 50mM PHOSPHATE BUFFER / pH: 3.5 / Pressure: 1 atm / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 150 / Conformers submitted total number: 15

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