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- PDB-1j26: Solution structure of a putative peptidyl-tRNA hydrolase domain i... -

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Basic information

Entry
Database: PDB / ID: 1j26
TitleSolution structure of a putative peptidyl-tRNA hydrolase domain in a mouse hypothetical protein
Componentsimmature colon carcinoma transcript 1
KeywordsTRANSLATION / peptide chain release factors / RF-1 / the GGQ motif / immature colon carcinoma transcript 1 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational termination / translation release factor activity, codon nonspecific / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / mitochondrion
Similarity search - Function
Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase ICT1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsNameki, N. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Solution structure of the catalytic domain of the mitochondrial protein ICT1 that is essential for cell vitality
Authors: Handa, Y. / Hikawa, Y. / Tochio, N. / Kogure, H. / Inoue, M. / Koshiba, S. / Guntert, P. / Inoue, Y. / Kigawa, T. / Yokoyama, S. / Nameki, N.
History
DepositionDec 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: immature colon carcinoma transcript 1


Theoretical massNumber of molelcules
Total (without water)12,1531
Polymers12,1531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein immature colon carcinoma transcript 1


Mass: 12152.575 Da / Num. of mol.: 1 / Fragment: peptidyl-tRNA hydrolase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NIA Mouse 15K cDNA Clone: H3024H01 / Plasmid: P020715-17 / Production host: Cell-free protein synthesis / References: UniProt: Q8R035

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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

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Sample preparation

DetailsContents: 1.7mM peptidyl-tRNA hydrolase domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.704Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpGuentert, P.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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