BMRB Entry 17710

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17710
MolProbity Validation Chart

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Title:
Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data
Deposition date:
2011-06-15
Original release date:
2011-10-12
Authors:
Tang, Ming; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Nesbitt, Anna; Nieuwkoop, Andrew; Gennis, Robert; Rienstra, Chad
Citation:

Citation: Tang, Ming; Sperling, Lindsay; Berthold, Deborah; Schwieters, Charles; Nesbitt, Anna; Nieuwkoop, Andrew; Gennis, Robert; Rienstra, Chad. "High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data."  J. Biomol. NMR 51, 227-233 (2011).
PubMed: 21938394

Assembly members:

Assembly members:
DsbA, polymer, 188 residues, 20993.951 Da.
DsbB, polymer, 176 residues, 15287.664 Da.
ZN, non-polymer, 65.409 Da.
UQ8, non-polymer, 727.109 Da.

Natural source:

Natural source:   Common Name: E. coli   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: pQE70

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DsbA: AQYEDGKQYTTLEKPVAGAP QVLEFFSFFCPHCYQFEEVL HISDNVKKKLPEGVKMTKYH VNFMGGDLGKDLTQAWAVAM ALGVEDKVTVPLFEGVQKTQ TIRSASDIRDVFINAGIKGE EYDAAWNSFVVKSLVAQQEK AAADVQLRGVPAMFVNGKYQ LNPQGMDTSNMDVFVQQYAD TVKYLSEK
DsbB: MLRFLNQASQGRGAWLLMAF TALALELTALWFQHVMLLKP SVLCIYERVALFGVLGAALI GAIAPKTPLRYVAMVIWLYS AFRGVQLTYEHTMLQLYPSP FATCDFMVRFPEWLPLDKWV PQVFVASGDCAERQWDFLGL EMPQWLLGIFIAYLIVAVLV VISQPFKAKKRDLFGR

Data sets:
Data typeCount
13C chemical shifts1228
15N chemical shifts288
1H chemical shifts67

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DsbA1
2DsbB2
3ZINC ION3
4UBIQUINONE-14

Entities:

Entity 1, DsbA 188 residues - 20993.951 Da.

1   ALAGLNTYRGLUASPGLYLYSGLNTYRTHR
2   THRLEUGLULYSPROVALALAGLYALAPRO
3   GLNVALLEUGLUPHEPHESERPHEPHECYS
4   PROHISCYSTYRGLNPHEGLUGLUVALLEU
5   HISILESERASPASNVALLYSLYSLYSLEU
6   PROGLUGLYVALLYSMETTHRLYSTYRHIS
7   VALASNPHEMETGLYGLYASPLEUGLYLYS
8   ASPLEUTHRGLNALATRPALAVALALAMET
9   ALALEUGLYVALGLUASPLYSVALTHRVAL
10   PROLEUPHEGLUGLYVALGLNLYSTHRGLN
11   THRILEARGSERALASERASPILEARGASP
12   VALPHEILEASNALAGLYILELYSGLYGLU
13   GLUTYRASPALAALATRPASNSERPHEVAL
14   VALLYSSERLEUVALALAGLNGLNGLULYS
15   ALAALAALAASPVALGLNLEUARGGLYVAL
16   PROALAMETPHEVALASNGLYLYSTYRGLN
17   LEUASNPROGLNGLYMETASPTHRSERASN
18   METASPVALPHEVALGLNGLNTYRALAASP
19   THRVALLYSTYRLEUSERGLULYS

Entity 2, DsbB 176 residues - 15287.664 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 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Entity 4, UBIQUINONE-1 - C49 H74 O4 - 727.109 Da.

1   UQ8

Samples:

sample_1: DsbA, [U-100% 13C; U-100% 15N], 15 mg; H2O 90%; D2O 10%

sample_2: DsbA, [2-13C-glycerol; U-15N], 10 mg; H2O 90%; D2O 10%

sample_3: DsbA, [1,3-13C-glycerol; U-15N], 10 mg; H2O 90%; D2O 10%

sample_4: DsbB, [U-100% 13C; U-100% 15N], 7 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%

sample_5: DsbB, [2-13C-glycerol; U-15N], 5 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%

sample_6: DsbB, [1,3-13C-glycerol; U-15N], 4 mg; DDM 2 mg; E. coli lipids 7 mg; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 270 K

sample_conditions_2: 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
2D CC DARRsample_4solidsample_conditions_2
2D CC DARRsample_5solidsample_conditions_2
2D CC DARRsample_6solidsample_conditions_2
3D NCACXsample_1solidsample_conditions_1
3D NCACXsample_2solidsample_conditions_1
3D NCACXsample_4solidsample_conditions_2
3D NCOCXsample_1solidsample_conditions_1
3D NCOCXsample_3solidsample_conditions_1
3D NCOCXsample_4solidsample_conditions_2
3D CAN(CO)CXsample_1solidsample_conditions_1
3D CAN(CO)CXsample_4solidsample_conditions_2
3D CON(CA)CXsample_4solidsample_conditions_2
4D CANCOCXsample_1solidsample_conditions_1
2D NC TEDORsample_3solidsample_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:

BMRB 16327 18396 18543 18544 15546 15966 18395 18493 18544
PDB
DBJ BAB38206 BAE77448 BAG79665 BAI27892 BAI33015 BAA36032 BAB35103 BAG76757 BAI24997 BAI30121
EMBL CAA44868 CAA56736 CAA90910 CAP78318 CAQ34212 CAP75720 CAQ31687 CAQ98064 CAR02574 CAR12682
GB AAA23715 AAB02995 AAC43519 AAC43520 AAC43521 AAA23711 AAB25233 AAC74269 AAG56036 AAN42789
REF NP_312810 NP_418297 NP_709659 WP_000725331 WP_000725332 NP_287424 NP_309707 NP_415703 NP_707082 NP_753538
SP P0A4L5 P0A4L6 P0AEG4 P0AEG5 P52235 A1AAA8 P0A6M2 P0A6M3 P59343 Q0T5L6
PIR H85696
AlphaFold P0A4L5 P0A4L6 P0AEG4 P0AEG5 P52235 A1AAA8 P0A6M2 P0A6M3 P59343 Q0T5L6

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