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BMRB Entry 15139

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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/BMR15139
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Title: NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100

Deposition date: 2007-02-21 Original release date: 2007-03-29

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 typeCount
13C chemical shifts491
15N chemical shifts119
1H chemical shifts785

Time Domain Data

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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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:

SWS P0A9I8

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts