BMRB Entry 34826

Title:
Structure of the dimeric, periplasmic domain of ExbD
Deposition date:
2023-06-14
Original release date:
2023-10-31
Authors:
Zinke, M.; Bardiaux, B.; Izadi-Pruneyre, N.
Citation:

Citation: Zinke, M.; Lejeune, M.; Mechaly, A.; Bardiaux, B.; Boneca, I.; Delepelaire, P.; Izadi-Pruneyre, N.. "Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake."  Biorxiv ., .-. (2023).
PubMed: 37609138

Assembly members:

Assembly members:
entity_1, polymer, 99 residues, 10870.383 Da.

Natural source:

Natural source:   Common Name: Serratia marcescens   Taxonomy ID: 615   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Serratia marcescens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pet30(a)+

Data sets:
Data typeCount
13C chemical shifts876
15N chemical shifts198
1H chemical shifts1394

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21

Entities:

Entity 1, unit_1 99 residues - 10870.383 Da.

1   SERVALASPILEARGVALASPLEUPROALA
2   SERSERALALYSPROGLNPROARGPROGLU
3   LYSPROVALPHELEUSERVALLYSALAASP
4   LYSGLNLEUTYRVALGLYASPGLNPROVAL
5   ASNALAASPGLNLEUTHRSERVALLEUASP
6   GLNARGTHRGLNALAASNLYSGLUTHRTHR
7   ILEPHEPHEGLNALAASPLYSSERVALASP
8   TYRGLUTHRLEUMETSERVALMETASPTHR
9   LEUARGLYSALAGLYTYRLEULYSVALGLY
10   LEUVALGLYMETGLUGLYALAALALYS

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM

sample_2: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM

sample_3: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H], 2 mM

sample_4: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H; natural abundance], 2 mM

sample_conditions_1: ionic strength: 0.3 mM; pH: 7; pressure: 1 atm; temperature: 293.15 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D hbCBcgcdHDsample_1isotropicsample_conditions_1
2D hbCBcgcdceHEsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D HNCO hydrogen bond detectionsample_3isotropicsample_conditions_1
3D DOUBLY-FILTERED 1H-13C NOESYsample_4isotropicsample_conditions_1
3D DOUBLY-FILTERED 1H-15N NOESYsample_4isotropicsample_conditions_1

Software:

CcpNmr Analysis Assign v3.1, Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW - chemical shift assignment

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA v2.3.3, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis v2.5, Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED - peak picking

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

TALOS-N v4.12, Shen and Bax - data analysis

NMR spectrometers:

  • Bruker AVANCE NEO 800 MHz
  • Bruker AVANCE III HD 600 MHz

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