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- PDB-1iyy: NMR STRUCTURE OF Gln25-RIBONUCLEASE T1, 24 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1iyy
TitleNMR STRUCTURE OF Gln25-RIBONUCLEASE T1, 24 STRUCTURES
ComponentsRIBONUCLEASE T1
KeywordsHYDROLASE / RIBONUCLEASE / ENDONUCLEASE / ENDORIBONUCLEASE
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / RNA endonuclease activity / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Synthetic ribonuclease T1 gene from Aspergillus oryzae / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsHatano, K. / Kojima, M. / Suzuki, E. / Tanokura, M. / Takahashi, K.
Citation
Journal: Biol. Chem. / Year: 2003
Title: Determination of the NMR structure of Gln25-ribonuclease T1.
Authors: Hatano, K. / Kojima, M. / Suzuki, E. / Tanokura, M. / Takahashi, K.
#1: Journal: J. Biochem. / Year: 1995
Title: Effects of replacement of Lys25 with Gln on the conformation of ribonuclease T1: sequence-specific 1H NMR resonance assignments of Gln25 ribonuclease T1 by two-dimensional NMR spectroscopy.
Authors: Kojima, M. / Miyano, H. / Suzuki, E. / Tanokura, M. / Takahashi, K.
History
DepositionSep 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)11,0941
Polymers11,0941
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5960 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50structures with the lowest energy
Representative

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Components

#1: Protein RIBONUCLEASE T1 / / GUANYLORIBONUCLEASE / RNASE T1


Mass: 11093.644 Da / Num. of mol.: 1 / Mutation: K25Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli)
References: UniProt: A2NUJ9, UniProt: P00651*PLUS, EC: 3.1.27.3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Structures were refined by 1340 NOES (392 INTRARESIDUE, 384 SEQUENTIAL AND 564 LONG-RANGE NOES) using A DG/SA protocol. 37 assignments for 14 CHI-1 ANGLE, 21 PHI ANGLE AND 2 OMEGA ANGLE ...Text: Structures were refined by 1340 NOES (392 INTRARESIDUE, 384 SEQUENTIAL AND 564 LONG-RANGE NOES) using A DG/SA protocol. 37 assignments for 14 CHI-1 ANGLE, 21 PHI ANGLE AND 2 OMEGA ANGLE constraints were included during the course of the refinement.

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Sample preparation

DetailsContents: 2mM Ribonuclease T1 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
X-PLOR3.1refinement
X-PLOR3.1structure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 24

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