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Biological Magnetic Resonance Data Bank


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BMRB Entry 5596

Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR5596

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Title: Solution Structure of the hypothetical protein yggU from E. coli. Northeast Structural Genomics Consortium Target ER14.

Deposition date: 2002-11-21 Original release date: 2003-09-05

Authors: Aramini, James; Xiao, Rong; Huang, Y.; Acton, Thomas; Wu, Maggie; Mills, Jeffrey; Tejero, Roberto; Szyperski, Thomas; Montelione, Gaetano

Citation: Aramini, James; Mills, Jeffrey; Xiao, Rong; Acton, Thomas; Wu, Maggie; Szyperski, Thomas; Montelione, Gaetano. "Letter to the Editor: Resonance assignments for the hypothetical protein yggU from Escherichia coli "  J. Biomol. NMR 27, 285-286 (2003).

Assembly members:
yggu_ecoli, polymer, 108 residues, 11883 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):
yggu_ecoli: MDGVMSAVTVNDDGLVLRLY IQPKASRDSIVGLHGDEVKV AITAPPVDGQANSHLVKFLG KQFRVAKSQVVIEKGELGRH KQIKIINPQQIPPEVAALIN LEHHHHHH

Data sets:
Data typeCount
1H chemical shifts752
13C chemical shifts454
15N chemical shifts108
coupling constants27

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ER141

Entities:

Entity 1, ER14 108 residues - 11883 Da.

1   METASPGLYVALMETSERALAVALTHRVAL
2   ASNASPASPGLYLEUVALLEUARGLEUTYR
3   ILEGLNPROLYSALASERARGASPSERILE
4   VALGLYLEUHISGLYASPGLUVALLYSVAL
5   ALAILETHRALAPROPROVALASPGLYGLN
6   ALAASNSERHISLEUVALLYSPHELEUGLY
7   LYSGLNPHEARGVALALALYSSERGLNVAL
8   VALILEGLULYSGLYGLULEUGLYARGHIS
9   LYSGLNILELYSILEILEASNPROGLNGLN
10   ILEPROPROGLUVALALAALALEUILEASN
11   LEUGLUHISHISHISHISHISHIS

Samples:

sample_1: yggu_ecoli, [U-100% 13C; U-100% 15N], 1.0 mM; MES 20 mM; NaCL 50 mM; DTT 5 mM; D2O 5%

sample_conditions_1: pH: 6.5; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
1H-15N-HSQC (regular)sample_1not availablesample_conditions_1
1H-13C-HSQC (aliphatic)sample_1not availablesample_conditions_1
3D 1H-15N NOESYsample_1not availablesample_conditions_1
3D 1H-13C NOESY (aliphatic)sample_1not availablesample_conditions_1
HNCOsample_1not availablesample_conditions_1
HNCAsample_1not availablesample_conditions_1
HN(CO)CAsample_1not availablesample_conditions_1
HN(CO)CACBsample_1not availablesample_conditions_1
HNCACBsample_1not availablesample_conditions_1
HA(CA)NHsample_1not availablesample_conditions_1
HA(CACO)NHsample_1not availablesample_conditions_1
(H)CC(CO)NH TOCSYsample_1not availablesample_conditions_1
H(CCCO)NH TOCSYsample_1not availablesample_conditions_1
HCCH COSY RD (sub1)sample_1not availablesample_conditions_1
HN RDsample_1not availablesample_conditions_1
HACA(CO)NH RD (sub1)sample_1not availablesample_conditions_1
HBCBHACA(CO)NH RD (sub1)sample_1not availablesample_conditions_1
HBCBHACACOHA RD (sub1)sample_1not availablesample_conditions_1
HBCBcgcdHD RD (sub1)sample_1not availablesample_conditions_1
H-TOCSY-CH-COSY RDsample_1not availablesample_conditions_1
1H-15N HSQC-J J=40mssample_1not availablesample_conditions_1
1H-15N-HSQC (NH2 only)sample_1not availablesample_conditions_1
1H-15N-HSQC (full SW)sample_1not availablesample_conditions_1
1H-15N-HSQC (MEXICO)sample_1not availablesample_conditions_1
1H-13C-HSQC (aromatic)sample_1not availablesample_conditions_1
3D 1H-13C NOESY (aromatic)sample_1not availablesample_conditions_1
HCCH COSY RD (sub2)sample_1not availablesample_conditions_1
HACA(CO)NH RD (sub2)sample_1not availablesample_conditions_1
HBCBHACA(CO)NH RD (sub2)sample_1not availablesample_conditions_1
HCCH COSY (regular)sample_1not availablesample_conditions_1
HBCBcgcdHD RD (sub2)sample_1not availablesample_conditions_1
HBCBHACACOHA RD (sub2)sample_1not availablesample_conditions_1
1H-15N HSQC-J J=56mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=33mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=50mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=70mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=83mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=100mssample_1not availablesample_conditions_1
1H-15N HSQC-J tauJ=125mssample_1not availablesample_conditions_1

Software:

VNMR v6.1B - spectrometer, acquisition

NMRPipe v2.1 - data processing

Sparky v3.106 - peak picking

AUTOASSIGN - automated assignment of backbone 1H, 13C, 15N chemical shifts

AUTOSTRUCTURE v1.1.2 - automated NOESY assignment and structure determination

HYPER v2.70 - data analysis

TALOS v2.1 - data analysis

DYANA v1.5 - structure refinement

XPLOR v2.0.4 (NIH) - structure refinement

PDBStat v3.27 - structure analysis

NMR spectrometers:

  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 750 MHz

Related Database Links:

PDB
DBJ BAB37252 BAE77016 BAG66691 BAG78745 BAI27237
EMBL CAP77390 CAQ33263 CAQ90385 CAQ99901 CAR04470
GB AAA69120 AAC75990 AAG58084 AAN44425 AAN81987
REF NP_289525 NP_311856 NP_417428 NP_708718 NP_755414
SP A1AFD9 B1IT54 B1LDG2 B1XFB3 B5YQF1

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