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 18493

Title: High resolution structure of DsbB C41S by joint calculation with solid-state NMR and X-ray data   PubMed: 23416557

Authors: Tang, Ming; Sperling, Lindsay; Schwieters, Charles; Nesbitt, Anna; Gennis, Robert; Rienstra, Chad

Citation: Tang, Ming; Nesbitt, Anna; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Gennis, Robert; Rienstra, Chad. "Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer."  J. Mol. Biol. 425, 1670-1682 (2013).

Assembly members:
DsbB, polymer, 176 residues, 16663.053 Da.
entity_2, polymer, 239 residues, 24077.834 Da.
entity_3, polymer, 221 residues, 23024.885 Da.
entity_UQ1, non-polymer, 250.290 Da.

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):
DsbB: MLRFLNQASQGRGAWLLMAF TALALELTALWFQHVMLLKP SVLCIYERVALFGVLGAALI GAIAPKTPLRYVAMVIWLYS AFRGVQLTYEHTMLQLYPSP FATCDFMVRFPEWLPLDKWV PQVFVASGDCAERQWDFLGL EMPQWLLGIFIAYLIVAVLV VISQPFKAKKRDLFGR
entity_2: MDSQAQVLILLLLWVSGTCG DIVMSQSPSSLAVSAGEKVT MSCKSSQSLLNSRTRKNYLA WYQQKPGQSPKLLIYWASTR ESGVPDRFTGSGSGTDFTLT ISSVQAEDLAVYYCKQSYNL YTFGGGTKLEIKRADAAPTV SIFPPSSEQLTSGGASVVCF LNNFYPKDINVKWKIDGSER QNGVLNSWTDQDSKDSTYSM SSTLTLTKDEYERHNSYTCE ATHKTSTSPIVKSFNRNEC
entity_3: EVQLVESGGGLVKPGGSLKL SCAASGFAFSSYDMSWVRQT PEKRLEWVAYISSGGGSTYY PDTVKGRFTISRDNAKNTLY LQMSSLKSEDTAMYYCARPD YRSYAMDYWGQGTSVTVSSA KTTAPSVYPLAPVCGDTTGS SVTLGCLVKGYFPEPVTLTW NSGSLSSGVHTFPAVLQSDL YTLSSSVTVTSSTWPSQSIT CNVAHPASSTKVDKKIEPRG P

Data sets:
Data typeCount
13C chemical shifts552
15N chemical shifts125
1H chemical shifts67

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DsbB_11
2entity_2_12
3entity_3_13
4DsbB_21
5entity_2_22
6entity_3_23
7UBIQUINONE-1_14
8UBIQUINONE-1_24

Entities:

Entity 1, DsbB_1 176 residues - 16663.053 Da.

1   METLEUARGPHELEUASNGLNALASERGLN
2   GLYARGGLYALATRPLEULEUMETALAPHE
3   THRALALEUALALEUGLULEUTHRALALEU
4   TRPPHEGLNHISVALMETLEULEULYSPRO
5   SERVALLEUCYSILETYRGLUARGVALALA
6   LEUPHEGLYVALLEUGLYALAALALEUILE
7   GLYALAILEALAPROLYSTHRPROLEUARG
8   TYRVALALAMETVALILETRPLEUTYRSER
9   ALAPHEARGGLYVALGLNLEUTHRTYRGLU
10   HISTHRMETLEUGLNLEUTYRPROSERPRO
11   PHEALATHRCYSASPPHEMETVALARGPHE
12   PROGLUTRPLEUPROLEUASPLYSTRPVAL
13   PROGLNVALPHEVALALASERGLYASPCYS
14   ALAGLUARGGLNTRPASPPHELEUGLYLEU
15   GLUMETPROGLNTRPLEULEUGLYILEPHE
16   ILEALATYRLEUILEVALALAVALLEUVAL
17   VALILESERGLNPROPHELYSALALYSLYS
18   ARGASPLEUPHEGLYARG

Entity 2, entity_2_1 239 residues - 24077.834 Da.

1   METASPSERGLNALAGLNVALLEUILELEU
2   LEULEULEUTRPVALSERGLYTHRCYSGLY
3   ASPILEVALMETSERGLNSERPROSERSER
4   LEUALAVALSERALAGLYGLULYSVALTHR
5   METSERCYSLYSSERSERGLNSERLEULEU
6   ASNSERARGTHRARGLYSASNTYRLEUALA
7   TRPTYRGLNGLNLYSPROGLYGLNSERPRO
8   LYSLEULEUILETYRTRPALASERTHRARG
9   GLUSERGLYVALPROASPARGPHETHRGLY
10   SERGLYSERGLYTHRASPPHETHRLEUTHR
11   ILESERSERVALGLNALAGLUASPLEUALA
12   VALTYRTYRCYSLYSGLNSERTYRASNLEU
13   TYRTHRPHEGLYGLYGLYTHRLYSLEUGLU
14   ILELYSARGALAASPALAALAPROTHRVAL
15   SERILEPHEPROPROSERSERGLUGLNLEU
16   THRSERGLYGLYALASERVALVALCYSPHE
17   LEUASNASNPHETYRPROLYSASPILEASN
18   VALLYSTRPLYSILEASPGLYSERGLUARG
19   GLNASNGLYVALLEUASNSERTRPTHRASP
20   GLNASPSERLYSASPSERTHRTYRSERMET
21   SERSERTHRLEUTHRLEUTHRLYSASPGLU
22   TYRGLUARGHISASNSERTYRTHRCYSGLU
23   ALATHRHISLYSTHRSERTHRSERPROILE
24   VALLYSSERPHEASNARGASNGLUCYS

Entity 3, entity_3_1 221 residues - 23024.885 Da.

1   GLUVALGLNLEUVALGLUSERGLYGLYGLY
2   LEUVALLYSPROGLYGLYSERLEULYSLEU
3   SERCYSALAALASERGLYPHEALAPHESER
4   SERTYRASPMETSERTRPVALARGGLNTHR
5   PROGLULYSARGLEUGLUTRPVALALATYR
6   ILESERSERGLYGLYGLYSERTHRTYRTYR
7   PROASPTHRVALLYSGLYARGPHETHRILE
8   SERARGASPASNALALYSASNTHRLEUTYR
9   LEUGLNMETSERSERLEULYSSERGLUASP
10   THRALAMETTYRTYRCYSALAARGPROASP
11   TYRARGSERTYRALAMETASPTYRTRPGLY
12   GLNGLYTHRSERVALTHRVALSERSERALA
13   LYSTHRTHRALAPROSERVALTYRPROLEU
14   ALAPROVALCYSGLYASPTHRTHRGLYSER
15   SERVALTHRLEUGLYCYSLEUVALLYSGLY
16   TYRPHEPROGLUPROVALTHRLEUTHRTRP
17   ASNSERGLYSERLEUSERSERGLYVALHIS
18   THRPHEPROALAVALLEUGLNSERASPLEU
19   TYRTHRLEUSERSERSERVALTHRVALTHR
20   SERSERTHRTRPPROSERGLNSERILETHR
21   CYSASNVALALAHISPROALASERSERTHR
22   LYSVALASPLYSLYSILEGLUPROARGGLY
23   PRO

Entity 4, UBIQUINONE-1_1 - C14 H18 O4 - 250.290 Da.

1   UQ1

Samples:

sample_1: DsbB, [U-100% 13C; U-100% 15N], 7 mg; DDM 2 mg; E. coli lipids 7 mg

sample_2: DsbB, [2-13C-glycerol; U-15N], 5 mg; DDM 2 mg; E. coli lipids 7 mg

sample_3: DsbB, [1,3-13C-glycerol; U-15N], 4 mg; DDM 2 mg; E. coli lipids 7 mg

sample_conditions_1: pH: 7.8; pressure: 1 atm; temperature: 261 K

Experiments:

NameSampleSample stateSample conditions
2D CC DARRsample_1solidsample_conditions_1
2D CC DARRsample_2solidsample_conditions_1
2D CC DARRsample_3solidsample_conditions_1
3D NCACXsample_1solidsample_conditions_1
3D NCOCXsample_1solidsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

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

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

TALOS+, Shen, Cornilescu, Delaglio and Bax - data analysis

VNMRJ, Varian - collection

NMR spectrometers:

  • Varian INOVA 750 MHz
  • Varian VXRS 500 MHz

Related Database Links:

PDB
BMRB 15546 15966 18395
DBJ BAA36032 BAB35103 BAG76757 BAI24997 BAI30121
EMBL CAP75720 CAQ31687 CAQ98064 CAR02574 CAR12682 CAA75918
GB AAA23711 AAB25233 AAC74269 AAG56036 AAN42789 AAA53292 AAB47613 AAL04472 AEB66102 EDK98900 AAN06761
PIR H85696 G33932 PS0023
REF NP_309707 NP_415703 NP_707082 WP_000652474 WP_000943442
SP A1AAA8 P0A6M2 P0A6M3 P59343 Q0T5L6