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- PDB-2k3r: Pfu Rpp21 structure and assignments -

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Basic information

Entry
Database: PDB / ID: 2k3r
TitlePfu Rpp21 structure and assignments
ComponentsRibonuclease P protein component 4
KeywordsHYDROLASE / Pfu Rpp21 / RNase P / tRNA processing
Function / homology
Function and homology information


ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / zinc ion binding / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #20 / Ribonuclease P subunit RNP4 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / N-terminal domain of TfIIb / Immunoglobulin FC, subunit C / Other non-globular / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonuclease P protein component 4
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsAmero, C.D. / Foster, M.P. / Boomershine, W.P. / Xu, Y.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner.
Authors: Amero, C.D. / Boomershine, W.P. / Xu, Y. / Foster, M.
History
DepositionMay 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease P protein component 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9882
Polymers14,9221
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ribonuclease P protein component 4 / RNase P component 4


Mass: 14922.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rnp4, PF1613 / Plasmid: pET-33b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U0H6, ribonuclease P
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1933D 1H-13C NOESY
11013D HBHA(CO)NH
11113D (H)CCH-COSY
11213D (H)CCH-TOCSY
11322D 1H-15N HSQC
11423D HNCO
11523D HNCA
11623D HN(CA)CB
11723D CBCA(CO)NH
11842D 1H-15N HSQC
11943D HNCO
12043D HNCA
12143D HN(CA)CB
12243D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM [U-99% 2H] TRIS, 10 mM potassium chloride, 0.02 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] Rpp21, 0.3 mM ZINC chloride, 90% H2O/10% D2O90% H2O/10% D2O
210 mM [U-99% 2H] TRIS, 10 mM potassium chloride, 0.02 % sodium azide, 0.5 mM [U-100% 13C; U-100% 15N] Rpp21, 0.3 mM ZINC chloride, 0.5 mM Rpp29, 90% H2O/10% D2O90% H2O/10% D2O
310 mM [U-99% 2H] TRIS, 10 mM potassium chloride, 0.02 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] Rpp21, 0.3 mM ZINC chloride, 100% D2O100% D2O
410 mM [U-99% 2H] TRIS, 10 mM potassium chloride, 0.02 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] Rpp21, 0.3 mM cobalt chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTRIS[U-99% 2H]1
10 mMpotassium chloride1
0.02 %sodium azide1
1 mMRpp21[U-100% 13C; U-100% 15N]1
0.3 mMZINC chloride1
10 mMTRIS[U-99% 2H]2
10 mMpotassium chloride2
0.02 %sodium azide2
0.5 mMRpp21[U-100% 13C; U-100% 15N]2
0.3 mMZINC chloride2
0.5 mMRpp292
10 mMTRIS[U-99% 2H]3
10 mMpotassium chloride3
0.02 %sodium azide3
1 mMRpp21[U-100% 13C; U-100% 15N]3
0.3 mMZINC chloride3
10 mMTRIS[U-99% 2H]4
10 mMpotassium chloride4
0.02 %sodium azide4
1 mMRpp21[U-100% 13C; U-100% 15N]4
0.3 mMcobalt chloride4
Sample conditionsIonic strength: 10 / pH: 6.7 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificstructure solution
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1352 / NOE intraresidue total count: 515 / NOE long range total count: 302 / NOE medium range total count: 154 / NOE sequential total count: 381
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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