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- PDB-2ki7: The solution structure of RPP29-RPP21 complex from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 2ki7
TitleThe solution structure of RPP29-RPP21 complex from Pyrococcus furiosus
Components
  • Ribonuclease P protein component 1
  • Ribonuclease P protein component 4
KeywordsHYDROLASE / RNase P / tRNA processing
Function / homology
Function and homology information


ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / rRNA processing / zinc ion binding / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #20 / Ribonuclease P/MRP, subunit p29 / Ribonuclease P subunit RNP4 / Ribonuclease P protein subunit RNP1 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 ...N-terminal domain of TfIIb - #20 / Ribonuclease P/MRP, subunit p29 / Ribonuclease P subunit RNP4 / Ribonuclease P protein subunit RNP1 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / 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 / 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 / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ribonuclease P protein component 1 / Ribonuclease P protein component 4
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXu, Y. / Foster, M.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and ...Title: Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.
Authors: Xu, Y. / Amero, C.D. / Pulukkunat, D.K. / Gopalan, V. / Foster, M.P.
History
DepositionApr 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease P protein component 1
B: Ribonuclease P protein component 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9703
Polymers29,9052
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 14982.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM3638 / JCM 8422 / Vc1 / Gene: rnp1, PF1816 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8U007, ribonuclease P
#2: 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 DSM 3638 (archaea) / Strain: DSM3638 / JCM 8422 / Vc1 / Gene: rnp4, PF1613 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8U0H6, ribonuclease P
#3: 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
1232D 1H-15N HSQC
1312D 1H-13C HSQC
1432D 1H-13C HSQC
1513D HNCO
1633D HNCO
1713D HN(CA)CB
1833D HN(CA)CB
1913D CBCA(CO)NH
11033D CBCA(CO)NH
11113D C(CO)NH TOCSY
11233D C(CO)NH TOCSY
11313D H(C)(CO)NH TOCSY
11433D H(C)(CO)NH TOCSY
11513D 1H-15N NOESY
11633D 1H-15N NOESY
21723D 1H-13C NOESY
21843D 1H-13C NOESY
21923D 13C-filtered/edited NOESY
22043D 13C-filtered/edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.25 mM [U-100% 13C; U-100% 15N] Pfu RPP29-1, 1.5 mM Pfu RPP21-2, 10 mM TRIS-3, 10 mM potassium chloride-4, 0.3 mM Zinc chloride-5, 0.02 % sodium azide-6, 10 % [U-99.8% 2H] D2O-7, 90 % H2O-8, 3 mM DSS-9, 90% H2O/10% D2O90% H2O/10% D2O
21.25 mM [U-100% 13C; U-100% 15N] Pfu RPP29-10, 1.5 mM Pfu RPP21-11, 10 mM TRIS-12, 10 mM potassium chloride-13, 0.3 % Zinc chloride-14, 0.02 % sodium azide-15, 100 % [U-99.8% 2H] D2O-16, 3 mM DSS-17, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] Pfu RPP21-18, 1.2 mM Pfu RPP29-19, 10 mM TRIS-20, 10 mM potassium chloride-21, 0.3 mM Zinc chloride-22, 0.02 % sodium azide-23, 90 % H2O-24, 10 % [U-99.8% 2H] D2O-25, 3 mM DSS-26, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] Pfu RPP21-27, 1.2 mM Pfu RPP29-28, 10 mM TRIS-29, 10 mM potassium chloride-30, 0.3 mM Zinc chloride-31, 0.02 % sodium azide-32, 100 % [U-99.8% 2H] D2O-33, 3 mM DSS-34, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMPfu RPP29-1[U-100% 13C; U-100% 15N]1
1.5 mMPfu RPP21-21
10 mMTRIS-31
10 mMpotassium chloride-41
0.3 mMZinc chloride-51
0.02 %sodium azide-61
10 %D2O-7[U-99.8% 2H]1
90 %H2O-81
3 mMDSS-91
1.25 mMPfu RPP29-10[U-100% 13C; U-100% 15N]2
1.5 mMPfu RPP21-112
10 mMTRIS-122
10 mMpotassium chloride-132
0.3 %Zinc chloride-142
0.02 %sodium azide-152
100 %D2O-16[U-99.8% 2H]2
3 mMDSS-172
1 mMPfu RPP21-18[U-100% 13C; U-100% 15N]3
1.2 mMPfu RPP29-193
10 mMTRIS-203
10 mMpotassium chloride-213
0.3 mMZinc chloride-223
0.02 %sodium azide-233
90 %H2O-243
10 %D2O-25[U-99.8% 2H]3
3 mMDSS-263
1 mMPfu RPP21-27[U-100% 13C; U-100% 15N]4
1.2 mMPfu RPP29-284
10 mMTRIS-294
10 mMpotassium chloride-304
0.3 mMZinc chloride-314
0.02 %sodium azide-324
100 %D2O-33[U-99.8% 2H]4
3 mMDSS-344
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.0475.8ambient 328 K
20.047ambient 328 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
XwinNMRBruker Biospincollection
CARAKeller R., Wuthrich K.chemical shift assignment
CARAKeller R., Wuthrich K.data analysis
SANEDuggan, Legge, Dyson & Wrightdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 4972 / NOE intraresidue total count: 1439 / NOE long range total count: 1497 / NOE medium range total count: 489 / NOE sequential total count: 839 / Protein phi angle constraints total count: 175 / Protein psi angle constraints total count: 175
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Torsion angle constraint violation method: Xplor-NIH
NMR ensemble rmsDistance rms dev: 0.035 Å / Distance rms dev error: 0.01 Å

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