BMRB Entry 15776

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15776
MolProbity Validation Chart

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Title:
Pfu Rpp21 structure and assignments
Deposition date:
2008-05-15
Original release date:
2008-11-14
Authors:
Amero, Carlos; Foster, Mark; Boomershine, William; Xu, Yiren
Citation:

Citation: Amero, Carlos; Boomershine, William; Xu, Yiren; Foster, Mark. "Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner"  Biochemistry 47, 11704-11710 (2008).
PubMed: 18922021

Assembly members:

Assembly members:
Rpp21, polymer, 123 residues, 65.409 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Pyrococcus furiosus   Taxonomy ID: 2261   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus furiosus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-33b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rpp21: MAKYNEKKEKKRIAKERIDI LFSLAERVFPYSPELAKRYV ELALLVQQKAKVKIPRKWKR RYCKKCHAFLVPGINARVRL RQKRMPHIVVKCLECGHIMR YPYIKEIKKRRKEKMEYGGL VPR

Data sets:
Data typeCount
13C chemical shifts370
15N chemical shifts75
1H chemical shifts558

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Rpp211
2Zn2

Entities:

Entity 1, Rpp21 123 residues - 65.409 Da.

1   METALALYSTYRASNGLULYSLYSGLULYS
2   LYSARGILEALALYSGLUARGILEASPILE
3   LEUPHESERLEUALAGLUARGVALPHEPRO
4   TYRSERPROGLULEUALALYSARGTYRVAL
5   GLULEUALALEULEUVALGLNGLNLYSALA
6   LYSVALLYSILEPROARGLYSTRPLYSARG
7   ARGTYRCYSLYSLYSCYSHISALAPHELEU
8   VALPROGLYILEASNALAARGVALARGLEU
9   ARGGLNLYSARGMETPROHISILEVALVAL
10   LYSCYSLEUGLUCYSGLYHISILEMETARG
11   TYRPROTYRILELYSGLUILELYSLYSARG
12   ARGLYSGLULYSMETGLUTYRGLYGLYLEU
13   VALPROARG

Entity 2, Zn - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: TRIS, [U-99% 2H], 10 mM; potassium chloride 10 mM; sodium azide 0.02%; Rpp21, [U-100% 13C; U-100% 15N], 1 mM; ZINC chloride 0.3 mM; H2O 90%; D2O 10%

sample_complex: TRIS, [U-99% 2H], 10 mM; potassium chloride 10 mM; sodium azide 0.02%; Rpp21, [U-100% 13C; U-100% 15N], 0.5 mM; ZINC chloride 0.3 mM; Rpp29 0.5 mM; H2O 90%; D2O 10%

sample_2: TRIS, [U-99% 2H], 10 mM; potassium chloride 10 mM; sodium azide 0.02%; Rpp21, [U-100% 13C; U-100% 15N], 1 mM; ZINC chloride 0.3 mM; H2O 90%; D2O 10%

sample_cobalt: TRIS, [U-99% 2H], 10 mM; potassium chloride 10 mM; sodium azide 0.02%; Rpp21, [U-100% 13C; U-100% 15N], 1 mM; cobalt chloride 0.3 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 10 mM; pH: 6.7; pressure: 1 atm; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_complexisotropicsample_conditions_1
3D HNCOsample_complexisotropicsample_conditions_1
3D HNCAsample_complexisotropicsample_conditions_1
3D HNCACBsample_complexisotropicsample_conditions_1
3D CBCA(CO)NHsample_complexisotropicsample_conditions_1
2D 1H-15N HSQCsample_cobaltisotropicsample_conditions_1
3D HNCOsample_cobaltisotropicsample_conditions_1
3D HNCAsample_cobaltisotropicsample_conditions_1
3D HNCACBsample_cobaltisotropicsample_conditions_1
3D 1H-15N NOESYsample_cobaltisotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

NMRView, Johnson, One Moon Scientific - data analysis, structure solution

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, structure solution

NMR spectrometers:

  • Bruker DRX 800 MHz
  • Bruker DMX 600 MHz

Related Database Links:

PDB
GB AAL81737 AFN05027
REF WP_011012760
SP Q8U0H6
AlphaFold Q8U0H6

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks