- PDB-2ki7: The solution structure of RPP29-RPP21 complex from Pyrococcus furiosus -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2ki7
Title
The solution structure of RPP29-RPP21 complex from Pyrococcus furiosus
Components
Ribonuclease P protein component 1
Ribonuclease P protein component 4
Keywords
HYDROLASE / RNase P / tRNA processing
Function / homology
Function and homology information
ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / RNA binding / 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 / 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. ...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 / 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
Journal: 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.
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
3
2D 1H-15N HSQC
1
3
1
2D 1H-13C HSQC
1
4
3
2D 1H-13C HSQC
1
5
1
3D HNCO
1
6
3
3D HNCO
1
7
1
3D HN(CA)CB
1
8
3
3D HN(CA)CB
1
9
1
3DCBCA(CO)NH
1
10
3
3DCBCA(CO)NH
1
11
1
3D C(CO)NH TOCSY
1
12
3
3D C(CO)NH TOCSY
1
13
1
3D H(C)(CO)NH TOCSY
1
14
3
3D H(C)(CO)NH TOCSY
1
15
1
3D 1H-15N NOESY
1
16
3
3D 1H-15N NOESY
2
17
2
3D 1H-13C NOESY
2
18
4
3D 1H-13C NOESY
2
19
2
3D 13C-filtered/edited NOESY
2
20
4
3D 13C-filtered/edited NOESY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.25 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% D2O
90% H2O/10% D2O
2
1.25 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% D2O
100% D2O
3
1 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% D2O
90% H2O/10% D2O
4
1 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% D2O
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1.25mM
Pfu RPP29-1
[U-100% 13C; U-100% 15N]
1
1.5mM
Pfu RPP21-2
1
10mM
TRIS-3
1
10mM
potassium chloride-4
1
0.3mM
Zinc chloride-5
1
0.02 %
sodium azide-6
1
10 %
D2O-7
[U-99.8% 2H]
1
90 %
H2O-8
1
3mM
DSS-9
1
1.25mM
Pfu RPP29-10
[U-100% 13C; U-100% 15N]
2
1.5mM
Pfu RPP21-11
2
10mM
TRIS-12
2
10mM
potassium chloride-13
2
0.3 %
Zinc chloride-14
2
0.02 %
sodium azide-15
2
100 %
D2O-16
[U-99.8% 2H]
2
3mM
DSS-17
2
1mM
Pfu RPP21-18
[U-100% 13C; U-100% 15N]
3
1.2mM
Pfu RPP29-19
3
10mM
TRIS-20
3
10mM
potassium chloride-21
3
0.3mM
Zinc chloride-22
3
0.02 %
sodium azide-23
3
90 %
H2O-24
3
10 %
D2O-25
[U-99.8% 2H]
3
3mM
DSS-26
3
1mM
Pfu RPP21-27
[U-100% 13C; U-100% 15N]
4
1.2mM
Pfu RPP29-28
4
10mM
TRIS-29
4
10mM
potassium chloride-30
4
0.3mM
Zinc chloride-31
4
0.02 %
sodium azide-32
4
100 %
D2O-33
[U-99.8% 2H]
4
3mM
DSS-34
4
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
0.047
5.8
ambient
328K
2
0.047
ambient
328K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DMX
Bruker
DMX
600
1
Bruker DRX
Bruker
DRX
800
2
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Processing
NMR software
Name
Developer
Classification
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
chemicalshiftcalculation
NMRView
Johnson, OneMoonScientific
peakpicking
NMRView
Johnson, OneMoonScientific
dataanalysis
XwinNMR
BrukerBiospin
collection
CARA
KellerR., WuthrichK.
chemicalshiftassignment
CARA
KellerR., WuthrichK.
dataanalysis
SANE
Duggan, Legge, Dyson & Wright
dataanalysis
TALOS
Cornilescu, DelaglioandBax
dataanalysis
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
structuresolution
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
dataanalysis
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
NOE 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 representative
Selection criteria: lowest energy
NMR ensemble
Conformer 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 rms
Distance rms dev: 0.035 Å / Distance rms dev error: 0.01 Å
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