7RY6

Solution NMR structural bundle of the first cyclization domain from yersiniabactin synthetase (Cy1) impacted by dynamics


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
11H,15N -TROSY588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
21H,15N -TROSY429 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 12 mg/mL Pf1 phage, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
31H,15N -TROSY586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
41H,15N -TROSY600 uM U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu delta-2, Val gamma-2, and Ile delta1 Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.03 % w/v Sodium Azide, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
51H,15N -TROSY600 uM U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu delta-2, Val gamma-2, and Ile delta1 Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.03 % w/v Sodium Azide, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 950
61H,15N -TROSY986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
73D HNCA588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
83D HNCA986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
93D HNCO588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
103D HNCO986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
113D HNCACO588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
123D HNCACO986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
133D HNCACB588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
143D HNCACB986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
363D HNCACB588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
153D HN(CO)CA588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
163D HN(CO)CA986 uM U-100% 13C, U-100% 15N; U-70% 2H; Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
173D HN(COCA)CB586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
193D Ala-HN(CA)CB586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
203D Gly-HNCA586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
213D Ser/Thr- HN(COCA)CB586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
373D Ser/Thr- HN(CA)CB586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
223D HMCMCBCA586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
233D HMCMCGCBCA586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
243D HCCCONH586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
383D HCCH-TOCSY586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
254D time-shared (TS) 15N/13C HSQC-NOESY-TROSY/ HSQC350 uM U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (delta-1), Leu (delta-1 and delta-2), and Val (gamma-1 and gamma-2) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
263D TS-TROSY/HSQC NOESY350 uM U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (delta-1), Leu (delta-1 and delta-2), and Val (gamma-1 and gamma-2) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
273D TS-NOESY -HSQC/TROSY350 uM U-100% 2H, U-100% 15N; 1H and 15N for Phe and Tyr; 1H and 13C for methyls of Ile (delta-1), Leu (delta-1 and delta-2), and Val (gamma-1 and gamma-2) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
283D TS-TROSY/HSQC NOESY600 uM U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu delta-2, Val gamma-2, and Ile delta1 Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.03 % w/v Sodium Azide, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 950
293D 15N TROSY-NOESY588 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
333D HSQC HNCO429 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 12 mg/mL Pf1 phage, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
343D TROSY HNCO429 uM [U-100% 13C; U-100% 15N; U-100% 2H] Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 12 mg/mL Pf1 phage, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Bruker AVANCE III 600
393D hNCAnH586 uM U-100% 13C; U-100% 15N; U-100% 2H; 1H,13C for methyls of Leu, Val and Ile (delta1) Cy1, 20 mM sodium phosphate, 10 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 0.25 mM DSS95% H2O/5% D2O10 mM NaCl mM7.01 atm298Varian UNITY 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III600
2VarianUNITY800
3BrukerAVANCE III950
NMR Refinement
MethodDetailsSoftware
molecular dynamicsThe structures are based on a total of 3468 restraints. 2189 are NOE based distance restraints, 293 are distance restraints based on hydrogen bonds, 810 are backbone dihedral angle restraints, and 176 are residual dipolar coupling restraints.CNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number500
Conformers Submitted Total Number20
Representative Model1 (medoid)
Additional NMR Experimental Information
DetailsThe authors state that the structural bundle reflects the fold of the cyclization domain with regions impacted by dynamics as described in the citation associated with this entry. Traditional analysis of individual conformers in the bundle is not recommended because dynamics may lead to apparent local distortions and because NMR structures of such large proteins rely on restraints involving backbone amides and methyl groups of Ile, Leu, and Val. All other side chains are deuterated and hence not experimentally restrained. The authors recommend that the ensemble is displayed as all states and aligned according to residues in secondary structures.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1chemical shift assignmentCARA1.9.1.4Keller and Wuthrich
2structure calculationCYANA3.98.13Guntert, Mumenthaler and Wuthrich
3refinementCNS1.3Brunger, Adams, Clore, Gros, Nilges and Read
4processingNMRPipe9.8Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5data analysisNMRFAM-SPARKY3.113T. D. Goddard and D. G. Kneller
6data analysisTALOS-NYang Shen and Ad Bax