BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15139

Title: NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100

Authors: Ramelot, Theresa; Cort, John; Yee, Adelinda; Guido, Valerie; Lukin, Jonathan; Arrowsmith, Cheryl; Kennedy, Michael

Citation: Ramelot, Theresa; Cort, John; Yee, Adelinda; Arrowsmith, Cheryl; Kennedy, Michael. "NMR structure of E.coli NirD."  . ., .-..

Assembly members:
NirD, polymer, 113 residues, 12750 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
NirD: QGHMSQWKDICKIDDILPET GVCALLGDEQVAIFRPYHSD QVFAISNIDPFFESSVLSRG LIAEHQGELWVASPLKKQRF RLSDGLCMEDEQFSVKHYEA RVKDGVVQLRGGS

Data sets:
  • assigned_chemical_shifts
Data typeCount
13C chemical shifts491
15N chemical shifts119
1H chemical shifts785

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1NirD1

Entities:

Entity 1, NirD 113 residues - 12750 Da.

Three non-native residues at the N-terminus (QGH), were not included in the calculation. Two non-native residues at the C-terminus (GS), were included in the calculation.

1   GLNGLYHISMETSERGLNTRPLYSASPILE
2   CYSLYSILEASPASPILELEUPROGLUTHR
3   GLYVALCYSALALEULEUGLYASPGLUGLN
4   VALALAILEPHEARGPROTYRHISSERASP
5   GLNVALPHEALAILESERASNILEASPPRO
6   PHEPHEGLUSERSERVALLEUSERARGGLY
7   LEUILEALAGLUHISGLNGLYGLULEUTRP
8   VALALASERPROLEULYSLYSGLNARGPHE
9   ARGLEUSERASPGLYLEUCYSMETGLUASP
10   GLUGLNPHESERVALLYSHISTYRGLUALA
11   ARGVALLYSASPGLYVALVALGLNLEUARG
12   GLYGLYSER

Samples:

sample_1: protein, [U-100% 13C], 1 ± .2 mM; TRIS 10 ± 1 mM; sodium chloride 300 ± 5 mM; ZINC ION 10 ± 1 uM; DTT 10 ± 1 mM; sodium azide 0.01 ± 0.001 %; H2O 95%; D2O 5%

sample_2: protein, [U-100% 13C], 1 ± .2 mM; TRIS 10 ± 1 mM; sodium chloride 300 ± 5 mM; ZINC ION 10 ± 1 uM; DTT 10 ± 1 mM; sodium azide 0.01 ± 0.001 %; D2O 100%

sample_conditions_1: ionic strength: 300 mM; pH: 7.3; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQC (NH2 only)sample_1isotropicsample_conditions_1
2D 1H-13C HSQC (aliph)sample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESY (aliph)sample_1isotropicsample_conditions_1
4D CC NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY (arom)sample_1isotropicsample_conditions_1
2D 1H-15N HSQC (open)sample_1isotropicsample_conditions_1
2D 1H-15N HSQC (optimized)sample_1isotropicsample_conditions_1
2D 1H-13C HSQC (arom ct)sample_1isotropicsample_conditions_1

Software:

AutoStruct v2.1.1, Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelione - data analysis

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

SPARKY v3.1, Goddard - peak picking

NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 750 MHz

Related Database Links:

BMRB 1514
PDB
DBJ BAB37640 BAE77924 BAG79152 BAI27625 BAI32795
EMBL CAA32417 CAP77819 CAQ33686 CAQ90816 CAR00306
GB AAA58163 AAC76391 AAG58474 AAN44848 AAN82580
REF NP_312244 NP_417825 NP_709141 WP_000084760 WP_000084761
SP P0A9I8 P0A9I9