BMRB Entry 18796

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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/BMR18796
MolProbity Validation Chart

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Title:
NMR structure of OmpX in phopspholipid nanodiscs
Deposition date:
2012-10-21
Original release date:
2012-12-10
Authors:
Hagn, Franz; Etzkorn, Manuel; Raschle, Thomas; Wagner, Gerhard
Citation:

Citation: Hagn, Franz; Etzkorn, Manuel; Raschle, Thomas; Wagner, Gerhard. "Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins."  J. Am. Chem. Soc. 135, 1919-1925 (2013).
PubMed: 23294159

Assembly members:

Assembly members:
OmpX, polymer, 148 residues, 16395.943 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
OmpX: ATSTVTGGYAQSDAQGQMNK MGGFNLKYRYEEDNSPLGVI GSFTYTEKSRTASSGDYNKN QYYGITAGPAYRINDWASIY GVVGVGYGKFQTTEYPTYKH DTSDYGFSYGAGLQFNPMEN VALDFSYEQSRIRSVDVGTW IAGVGYRF

Data sets:
Data typeCount
13C chemical shifts372
15N chemical shifts131
1H chemical shifts136

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1OmpX1

Entities:

Entity 1, OmpX 148 residues - 16395.943 Da.

1   ALATHRSERTHRVALTHRGLYGLYTYRALA
2   GLNSERASPALAGLNGLYGLNMETASNLYS
3   METGLYGLYPHEASNLEULYSTYRARGTYR
4   GLUGLUASPASNSERPROLEUGLYVALILE
5   GLYSERPHETHRTYRTHRGLULYSSERARG
6   THRALASERSERGLYASPTYRASNLYSASN
7   GLNTYRTYRGLYILETHRALAGLYPROALA
8   TYRARGILEASNASPTRPALASERILETYR
9   GLYVALVALGLYVALGLYTYRGLYLYSPHE
10   GLNTHRTHRGLUTYRPROTHRTYRLYSHIS
11   ASPTHRSERASPTYRGLYPHESERTYRGLY
12   ALAGLYLEUGLNPHEASNPROMETGLUASN
13   VALALALEUASPPHESERTYRGLUGLNSER
14   ARGILEARGSERVALASPVALGLYTHRTRP
15   ILEALAGLYVALGLYTYRARGPHE

Samples:

sample_1: potassium phosphate 20 mM; sodium chloride 50 mM; EDTA, [U-2H], 10 mM; sodium azide 0.05%; OmpX, [U-13C; U-15N; U-2H], 0.8 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

Software:

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

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 750 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 15201 18797 19892
PDB
DBJ BAA35486 BAB34315 BAG76394 BAI24257 BAI29701
EMBL CAP75284 CAQ31315 CAQ97717 CAR02170 CAR06985
GB AAA21856 AAA66329 AAC73901 AAG55186 AAN42399
REF NP_308919 NP_415335 NP_706692 WP_001295296 WP_001340109
SP P0A917 P0A918 P0A919 P0A920
AlphaFold P0A917 P0A918 P0A919 P0A920

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