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- PDB-1oqk: Structure of Mth11: A homologue of human RNase P protein Rpp29 -

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Basic information

Entry
Database: PDB / ID: 1oqk
TitleStructure of Mth11: A homologue of human RNase P protein Rpp29
Componentsconserved protein MTH11
KeywordsHYDROLASE / OB fold / archaeal RNase P protein subunit
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease P/MRP, subunit p29 / Ribonuclease P protein subunit RNP1 / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Ribonuclease P protein component 1
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsBoomershine, W.P. / McElroy, C.A. / Tsai, H. / Gopalan, V. / Foster, M.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2003
Title: Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.
Authors: Boomershine, W.P. / McElroy, C.A. / Tsai, H.Y. / Wilson, R.C. / Gopalan, V. / Foster, M.P.
History
DepositionMar 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_nmr_software
Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved protein MTH11


Theoretical massNumber of molelcules
Total (without water)11,1581
Polymers11,1581
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)22 / 35structures with the lowest energy
RepresentativeModel #1first structure in ensemble

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Components

#1: Protein conserved protein MTH11


Mass: 11157.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH11 / Plasmid: MTH11-PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: O26119, ribonuclease P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
1213D 13C-separated NOESY
1313D 15N-separated NOESY
1423D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Mth11 U-15N, 13C, 50mM phosphate buffer K, 50mM KCl, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM Mth11 U-15N, 13C, 50mM phosphate buffer K, 50mM KCl, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM / pH: 7.0 / Pressure: 1 atm / Temperature: 299 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 DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1Brungerrefinement
CNS1.1collection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: first structure in ensemble
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 22

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