BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 7274

Title: Solution NMR structure of the YdfO protein from Escherichia coli. Northeast Structural Genomics target ER251

Deposition date: 2006-08-24 Original release date: 2007-02-01

Authors: Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.

Citation: Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.. "Solution NMR structure of the YdfO protein from Escherichia coli. Northeast Structural Genomics target ER251"  .

Assembly members:
Hypothetical protein YdfO, polymer, 149 residues, Formula weight is not available

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

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

Entity Sequences (FASTA):
Hypothetical protein YdfO: MEGLSMDQVVIFKQIFDKVR NDLNYQWFYSELKRHNVSHY IYYLATENVHIVLKNDNTVL LKGLKNIVSVKFSKDRHLIE TTSNKLKSREITFQEYRRNL AKAGVFRWVTNIHEQKRYYY TFDNSLLFTESIQKTTQIFP RLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts680
15N chemical shifts168
1H chemical shifts1013

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Hypothetical protein YdfO1

Entities:

Entity 1, Hypothetical protein YdfO 149 residues - Formula weight is not available

1   METGLUGLYLEUSERMETASPGLNVALVAL
2   ILEPHELYSGLNILEPHEASPLYSVALARG
3   ASNASPLEUASNTYRGLNTRPPHETYRSER
4   GLULEULYSARGHISASNVALSERHISTYR
5   ILETYRTYRLEUALATHRGLUASNVALHIS
6   ILEVALLEULYSASNASPASNTHRVALLEU
7   LEULYSGLYLEULYSASNILEVALSERVAL
8   LYSPHESERLYSASPARGHISLEUILEGLU
9   THRTHRSERASNLYSLEULYSSERARGGLU
10   ILETHRPHEGLNGLUTYRARGARGASNLEU
11   ALALYSALAGLYVALPHEARGTRPVALTHR
12   ASNILEHISGLUGLNLYSARGTYRTYRTYR
13   THRPHEASPASNSERLEULEUPHETHRGLU
14   SERILEGLNLYSTHRTHRGLNILEPHEPRO
15   ARGLEUGLUHISHISHISHISHISHIS

Samples:

sample_1: Hypothetical protein YdfO, [U-13C; U-15N], 0.69 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 5%; H2O 95%

sample_2: Hypothetical protein YdfO, [U-5% 13C; U-15N], 0.74 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 5%; H2O 95%

sample_3: Hypothetical protein YdfO, [U-13C; U-15N], 0.69 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 99.9%

sample_cond_1: ionic strength: 0.1 M; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D 13C-separated NOESYnot availablenot availablenot available
3D 15N-separated NOESYnot availablenot availablenot available
HcCH-TOCSYnot availablenot availablenot available
HcCH-COSYnot availablenot availablenot available
CccoNH-TOCSYnot availablenot availablenot available
3D-HNCACBnot availablenot availablenot available
HNcoCACBnot availablenot availablenot available
HBHAcoNHnot availablenot availablenot available
HNCOnot availablenot availablenot available
13C HSQC noct Stereospecific VL Me assign.not availablenot availablenot available
Het-NOEnot availablenot availablenot available
T1/T1rhonot availablenot availablenot available

Software:

VNMR v6.1C - collection

xwinnmr v3.5 - collection

DYANA v1.2 - structure solution

X-PLOR v2.11.2 - refinement

NMRPipe v2005 - processing

SPARKY v3.11 - data analysis

AutoAssign v2.2.1 - data analysis

AutoStruct v2.1.1 - structure solution

HYPER v2.1 - structure solution

PDBStat v4.1 - data analysis

PSVS v1.3 - refinement

CNS v1.1 - refinement

Procheck NMR v3.51 - refinement

MolProbity v3.01 - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAE76466 BAJ43349
EMBL CAQ98449 CAR17640 CBG34523 CDJ71949 CDK69631
GB AAC74622 AAN79909 ACA77728 ACB02759 ACR65380
REF NP_416067 NP_753349 WP_000373089 WP_000373090 WP_000398761
SP P76156
AlphaFold P76156

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