6X6N | pdb_00006x6n

NMR structure of the putative GTPase-Activating (GAP) domain of VopE


SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion1
Scattering Typeneutron
Radiation/Neutron SourceAPS Beamline 18D
SynchrotronY
Beamline TypeAPS
Detector TypePilatus 3X 1M
Detector Manufacturer DetailsDectris
Temperature (K)298.15
pH7.4
Numer of Time Frames Used640
Protein Concentration Range (mg/mL)19.5
Sample Buffer10 mM HEPES*HCl pH 7.4, 150 mM NaCl, 0.5 mM TCEP
Data Reduction SoftwareGNOM
Guiner Mean Radius Of Gyration (nm)20.23
Sigma Mean Radius Of Gyration0.09
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)7.8
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
23D HNCACB0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
33D CBCA(CO)NH0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
43D HNCO0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
53D C(CO)NH0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
83D HBHA(CO)NH0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
73D HCCH-COSY0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
63D HCCH-TOCSY0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
92D 1H-13C HSQC0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
102D Aromatic 1H-13C HSQC0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
112D CBHD aromatic0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
142D CBHDHE aromatic0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
133D H(C)CH-TOCSY aromatic0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
122D ARTSY0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Bruker AVANCE III 750
163D 1H-13C NOESY aromatic0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
183D 1H-15N NOESY0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
173D 1H-13C NOESY0.960 mM [U-13C; U-15N] VopE GAP Domain, 10 mM HEPES pH 6.0, 150 mM sodium chloride, 0.5 mM TCEP, 10 v/v D2O90% H2O/10% D2O150 mM6.01 atm298Agilent Varian VNMRS 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1AgilentVarian VNMRS600
2BrukerAVANCE III750
NMR Refinement
MethodDetailsSoftware
simulated annealingPONDEROSA-C/S
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
2collectionVNMR4.2Varian
5collectionTopSpin3.5Bruker Biospin
3peak pickingNMRFAM-SPARKYWoonghee Lee, Marco Tonelli, John L Markley
6structure calculationPONDEROSA-C/SWoonghee Lee, Jaime L. Stark, John L. Markley
4structure calculationTALOS-NCornilescu, Delaglio and Bax
7structure calculationX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
8refinementPyMOLSchroedinger
9chemical shift assignmentNMRFAM-SPARKYWoonghee Lee, Marco Tonelli, John L Markley