9RTJ | pdb_00009rtj

Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP


SOLUTION NMR - SOLID-STATE NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D HNCA0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
23D HN(CA)CO0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
33D HN(CO)CA0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
43D HNCACB0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
53D CBCA(CO)NH0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
63D HNCO0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
73D C(CO)NH0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
83D H(CCO)NH0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE NEO 700
93D 1H-15N NOESY0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
103D 1H-13C NOESY aliphatic1.1 mM DNA, 1 mM [U-99% 13C; U-99% 15N] HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O75 mM7.01 atm298Bruker AVANCE III HD 900
113D 1H-13C NOESY aliphatic10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
123D 1H-13C NOESY aromatic10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
133D 1H-13C NOESY aromatic1.1 mM DNA, 1 mM [U-99% 13C; U-99% 15N] HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O75 mM7.01 atm298Bruker AVANCE III HD 900
142D 1H-13C HSQC aromatic10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
152D 1H-13C HSQC aliphatic10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
162D-F1fF2f-NOESY1 mM DNA, 1 mM [U-99% 13C; U-99% 15N] HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+100% D2O75 mM7.01 atm298Bruker AVANCE III HD 900
172D-F2f-NOESY1 mM DNA, 1 mM [U-99% 13C; U-99% 15N] HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+100% D2O75 mM7.01 atm298Bruker AVANCE III HD 900
183D-13C-aliphatic-HfilteredHedited-NOESY10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
193D-13C-aromatic-HfilteredHedited-NOESY10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
202D-imino-NOESY1 mM DNA, 1 mM HBD, 2 mM AppCp, 2 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O75 mM7.01 atm298Bruker AVANCE III HD 900
212D-natural-abundance-Nhsqc4 mM DNA, 4 mM HBD, 4 mM AppCp, 4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O120 mM7.01 atm298Bruker AVANCE NEO 600
222D-natural-abundance-Chsqc-aliphatic1 mM DNA, 1 mM HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+100% D2O75 mM7.01 atm298Bruker AVANCE NEO 700
232D-natural-abundance-Chsqc-aromatic1 mM DNA, 1 mM HBD, 1.2 mM AppCp, 1.2 mM dGppCp, 10 mM Mg2+100% D2O75 mM7.01 atm298Bruker AVANCE NEO 700
242D 1H-15N HSQC0.96 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 2.4 mM AppCp, 2.4 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
252D 1H-15N HSQC10.8 mM DNA, 0.8 mM [U-99% 13C; U-99% 15N] HBD, 1.6 mM AppCp, 1.6 mM dGppCp, 10 mM Mg2+100% D2O100 mM7.01 atm298Bruker AVANCE III HD 900
26CHHP2.5 mM DNA, 2.3 mM [U-100% 13C; U-100% 15N] pRN1 primase H145A, 4.6 mM AppCp, 4.6 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O50 mM7.01 atm278Bruker AVANCE III 500
27NHHP2.5 mM DNA, 2.3 mM [U-100% 13C; U-100% 15N] pRN1 primase H145A, 4.6 mM AppCp, 4.6 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O50 mM7.01 atm278Bruker AVANCE III 500
28hPH0.254 mM DNA, 0.231 mM [U-100% 15N; U-80% 2H] pRN1 primase H145A, 0.924 mM AppNHp, 0.924 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O50 mM7.01 atm278Bruker AVANCE III 850
29hPH0.254 mM DNA, 0.231 mM [U-15N; U-2H] pRN1 primase, 0.924 mM AppNHp, 0.924 mM dGppCp, 10 mM Mg2+90% H2O/10% D2O50 mM7.01 atm278Bruker AVANCE III 850
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III HD900
2BrukerAVANCE NEO700
3BrukerAVANCE NEO600
4BrukerAVANCE III500
5BrukerAVANCE III850
NMR Refinement
MethodDetailsSoftware
torsion angle dynamicsCYANA
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number500
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure calculationCYANA3.98.15Guntert, Mumenthaler and Wuthrich
2data analysisNMRFAM-SPARKY1.470Goddard
3peak pickingCANDIDHerrmann, Guntert and Wuthrich
4refinementAmber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
5collectionTopSpin4.0.7Bruker Biospin
6processingTopSpin4.0.7Bruker Biospin
7chemical shift assignmentNMRFAM-SPARKY1.470Goddard