BMRB Entry 30943

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30943
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Solution structure of first cyclization domain (Cy1) from yersiniabactin synthetase
Deposition date:
2021-08-24
Original release date:
2022-07-08
Authors:
Mishra, Subrata; Frueh, Dominique
Citation:

Citation: Mishra, Subrata; Kancherla, Aswani; Marincin, Kenneth; Bouvignies, Guillaume; Nerli, Santrupti; Sgourakis, Nikolaos; Dowling, Daniel; Frueh, Dominique. "Global protein dynamics as communication sensors in peptide synthetase domains"  Sci. Adv. 8, eabn6549-eabn6549 (2022).
PubMed: 35857508

Assembly members:

Assembly members:
entity_1, polymer, 453 residues, 51914.559 Da.

Natural source:

Natural source:   Common Name: Yersinia pestis   Taxonomy ID: 632   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Yersinia pestis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MPDESSWPNMTESTPFPLTP VQHAYLTGRMPGQTLGGVGC HLYQEFEGHCLTASQLEQAI TTLLQRHPMLHIAFRPDGQQ VWLPQPYWNGVTVHDLRHND AESRQAYLDALRQRLSHRLL RVEIGETFDFQLTLLPDNRH RLHVNIDLLIMDASSFTLFF DELNALLAGESLPAIDTRYD FRSYLLHQQKINQPLRDDAR AYWLAKASTLPPAPVLPLAC EPATLREVRNTRRRMIVPAT RWHAFSNRAGEYGVTPTMAL ATCFSAVLARWGGLTRLLLN ITLFDRQPLHPAVGAMLADF TNILLLDTACDGDTVSNLAR KNQLTFTEDWEHRHWSGVEL LRELKRQQRYPHGAPVVFTS NLGRSLYSSRAESPLGEPEW GISQTPQVWIDHLAFEHHGE VWLQWDSNDALFPPALVETL FDAYCQLINQLCDDESAWQK PFADMLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts1421
15N chemical shifts393
1H chemical shifts1374

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 453 residues - 51914.559 Da.

1   METPROASPGLUSERSERTRPPROASNMET
2   THRGLUSERTHRPROPHEPROLEUTHRPRO
3   VALGLNHISALATYRLEUTHRGLYARGMET
4   PROGLYGLNTHRLEUGLYGLYVALGLYCYS
5   HISLEUTYRGLNGLUPHEGLUGLYHISCYS
6   LEUTHRALASERGLNLEUGLUGLNALAILE
7   THRTHRLEULEUGLNARGHISPROMETLEU
8   HISILEALAPHEARGPROASPGLYGLNGLN
9   VALTRPLEUPROGLNPROTYRTRPASNGLY
10   VALTHRVALHISASPLEUARGHISASNASP
11   ALAGLUSERARGGLNALATYRLEUASPALA
12   LEUARGGLNARGLEUSERHISARGLEULEU
13   ARGVALGLUILEGLYGLUTHRPHEASPPHE
14   GLNLEUTHRLEULEUPROASPASNARGHIS
15   ARGLEUHISVALASNILEASPLEULEUILE
16   METASPALASERSERPHETHRLEUPHEPHE
17   ASPGLULEUASNALALEULEUALAGLYGLU
18   SERLEUPROALAILEASPTHRARGTYRASP
19   PHEARGSERTYRLEULEUHISGLNGLNLYS
20   ILEASNGLNPROLEUARGASPASPALAARG
21   ALATYRTRPLEUALALYSALASERTHRLEU
22   PROPROALAPROVALLEUPROLEUALACYS
23   GLUPROALATHRLEUARGGLUVALARGASN
24   THRARGARGARGMETILEVALPROALATHR
25   ARGTRPHISALAPHESERASNARGALAGLY
26   GLUTYRGLYVALTHRPROTHRMETALALEU
27   ALATHRCYSPHESERALAVALLEUALAARG
28   TRPGLYGLYLEUTHRARGLEULEULEUASN
29   ILETHRLEUPHEASPARGGLNPROLEUHIS
30   PROALAVALGLYALAMETLEUALAASPPHE
31   THRASNILELEULEULEUASPTHRALACYS
32   ASPGLYASPTHRVALSERASNLEUALAARG
33   LYSASNGLNLEUTHRPHETHRGLUASPTRP
34   GLUHISARGHISTRPSERGLYVALGLULEU
35   LEUARGGLULEULYSARGGLNGLNARGTYR
36   PROHISGLYALAPROVALVALPHETHRSER
37   ASNLEUGLYARGSERLEUTYRSERSERARG
38   ALAGLUSERPROLEUGLYGLUPROGLUTRP
39   GLYILESERGLNTHRPROGLNVALTRPILE
40   ASPHISLEUALAPHEGLUHISHISGLYGLU
41   VALTRPLEUGLNTRPASPSERASNASPALA
42   LEUPHEPROPROALALEUVALGLUTHRLEU
43   PHEASPALATYRCYSGLNLEUILEASNGLN
44   LEUCYSASPASPGLUSERALATRPGLNLYS
45   PROPHEALAASPMETLEUGLUHISHISHIS
46   HISHISHIS

Samples:

sample_1: Cy1, [U-100% 13C; U-100% 15N; U-100% 2H], 588 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM

sample_2: Cy1, [U-100% 13C; U-100% 15N; U-100% 2H], 429 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM; Pf1 phage 12 mg/mL

sample_3: Cy1, [U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (D1)], 586 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM

sample_4: Cy1, [U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu D2, Val G2, and Ile D1], 600 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM; Sodium Azide 0.03 % w/v

sample_5: Cy1, [U-100% 13C, U-100% 15N; U-70% 2H], 986 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM

sample_6: Cy1, [U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (D1), Leu (D1 and D2), and Val (G1 and G2)], 350 uM; sodium phosphate 20 mM; sodium chloride 10 mM; EDTA 1 mM; DTT 5 mM; DSS 0.25 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
1H,15N -TROSYsample_1isotropicsample_conditions_1
1H,15N -TROSYsample_2isotropicsample_conditions_1
1H,15N -TROSYsample_3isotropicsample_conditions_1
1H,15N -TROSYsample_4isotropicsample_conditions_1
1H,15N -TROSYsample_4isotropicsample_conditions_1
1H,15N -TROSYsample_5isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCAsample_5isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCOsample_5isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D HNCACOsample_5isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_5isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_5isotropicsample_conditions_1
3D HN(COCA)CBsample_3isotropicsample_conditions_1
3D Ala-HN(CA)CBsample_3isotropicsample_conditions_1
3D Gly-HNCAsample_3isotropicsample_conditions_1
3D Ser/Thr- HN(COCA)CBsample_3isotropicsample_conditions_1
3D HMCMCBCAsample_3isotropicsample_conditions_1
3D HMCMCGCBCAsample_3isotropicsample_conditions_1
3D HCCCONHsample_3isotropicsample_conditions_1
4D time-shared (TS) 15N/13C HSQC-NOESY-TROSY/ HSQCsample_6isotropicsample_conditions_1
3D TS-TROSY/HSQC NOESYsample_6isotropicsample_conditions_1
3D TS-NOESY -HSQC/TROSYsample_6isotropicsample_conditions_1
3D TS-TROSY/HSQC NOESYsample_4isotropicsample_conditions_1
3D 15N TROSY-NOESYsample_1isotropicsample_conditions_1
3D HSQC HNCOsample_2anisotropicsample_conditions_1
3D TROSY HNCOsample_2anisotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D Ser/Thr- HN(CA)CBsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D hNCAnHsample_3isotropicsample_conditions_1

Software:

CARA v1.9.1.4, Keller and Wuthrich - chemical shift assignment

CYANA v3.98.13, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRPipe v9.8, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRFAM-SPARKY v3.113, T. D. Goddard and D. G. Kneller - data analysis

TALOS-N, Yang Shen and Ad Bax - data analysis

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Varian UNITY 800 MHz
  • Bruker AVANCE III 950 MHz

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