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- PDB-2ljp: Backbone 1H, 13C, and 15N Chemical Shift Assignments for E.coli R... -

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Basic information

Entry
Database: PDB / ID: 2ljp
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for E.coli Ribonuclease P protein
ComponentsRibonuclease P protein component
KeywordsHYDROLASE / RNaseP / C5 / ribonuclease P / Ribozyme
Function / homology
Function and homology information


: / 3'-tRNA processing endoribonuclease activity / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA processing / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsShin, J. / Kim, K. / Ryu, K. / Han, K. / Lee, Y. / Choi, B.
CitationJournal: To be Published
Title: Structural analysis of Escherichia coli C5 protein
Authors: Shin, J. / Kim, K. / Ryu, K. / Han, K. / Lee, Y. / Choi, B.
History
DepositionSep 21, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease P protein component


Theoretical massNumber of molelcules
Total (without water)13,8181
Polymers13,8181
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease P protein component / RNase P protein / RNaseP protein / Protein C5


Mass: 13818.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rnpA, b3704, JW3681 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y8, ribonuclease P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D 1H-13C NOESY aliphatic
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-95% 13C; U-95% 15N] E.coli Ribonuclease P protein-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: E.coli Ribonuclease P protein-1 / Isotopic labeling: [U-95% 13C; U-95% 15N]
Sample conditionsIonic strength: 0.2 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddarddata analysis
CNS1.21refinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 84 / Protein psi angle constraints total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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