BMRB Entry 30153

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30153
MolProbity Validation Chart

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Title:
The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE)
Deposition date:
2016-08-10
Original release date:
2016-11-23
Authors:
Evans, R.; Xia, Y.; Wilmot, C.
Citation:

Citation: Evans, R.; Latham, J.; Klinman, J.; Xia, Y.; Wilmot, C.; Evans, R.; Latham, J.; Klinman, J.; Wilmot, C.; Xia, Y.. "(1)H, (13)C, and (15)N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA"  Biomol. NMR Assign. 10, 385-389 (2016).
PubMed: 27638737

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, 10421.945 Da.

Natural source:

Natural source:   Common Name: Methylobacterium extorquens   Taxonomy ID: 272630   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Methylobacterium extorquens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MEPTAFSGSDVPRLPRGVRL RFDEVRNKHVLLAPERTFDL DDNAVAVLKLVDGRNTVSQI AQILGQTYDADPAIIEADIL PMLAGLAQKRVLER

Data sets:
Data typeCount
13C chemical shifts405
15N chemical shifts87
1H chemical shifts647

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 94 residues - 10421.945 Da.

1   METGLUPROTHRALAPHESERGLYSERASP
2   VALPROARGLEUPROARGGLYVALARGLEU
3   ARGPHEASPGLUVALARGASNLYSHISVAL
4   LEULEUALAPROGLUARGTHRPHEASPLEU
5   ASPASPASNALAVALALAVALLEULYSLEU
6   VALASPGLYARGASNTHRVALSERGLNILE
7   ALAGLNILELEUGLYGLNTHRTYRASPALA
8   ASPPROALAILEILEGLUALAASPILELEU
9   PROMETLEUALAGLYLEUALAGLNLYSARG
10   VALLEUGLUARG

Samples:

sample_1: PqqD, [U-13C; U-15N], 4.6 mg/mL; potassium phosphate 25 mM

sample_conditions_1: ionic strength: 25 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
2D plane of 3D HCACOsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D HBCBCGCDHDsample_1isotropicsample_conditions_1
2D HBCBCGCDCEHEsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D plane of HCCH-TOCSY for aromatic ringsample_1isotropicsample_conditions_1
3D 15N-edited NOESYsample_1isotropicsample_conditions_1
3D 13C-edited NOESYsample_1isotropicsample_conditions_1

Software:

NMRPipe vyear 2012, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Protein Structure Validation Suite (PSVS) v1.5, http://psvs-1_5-dev.nesg.org/ - refinement

SPARKY v3, Goddard and Kneller - data analysis

TOPSPIN v3.1.6, Bruker Biospin - collection

XPLOR-NIH v2.37, Schwieters - structure calculation

NMR spectrometers:

  • Bruker AvanceIII 850 MHz
  • Bruker AvanceIII 900 MHz

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