2JOQ | pdb_00002joq

Solution Structure of Protein HP0495 from H. pylori; Northeast structural genomics consortium target PT2; Ontario Centre for Structural Proteomics target HP0488


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
22D 1H-13C HSQC0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
33D CBCA(CO)NH0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
43D HNCO sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
53D HNCA sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
63D H(CCCO)NH-TOCSY sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
73D (H)C(CCO)NH-TOCSY0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
84D HBHACBCA(CO)NH PR0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
94D HC(CCO)NH-TOCSY PR0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
103D 1H-15N NOESY sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
113D 1H-13C NOESY aliphatic0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
123D H(C)CH-TOCSY sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
133D (H)CCH-TOCSY sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
143D 1H-13C NOESY aromatic0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide95% H2O/5% D2O3007ambient298
153D 1H-13C NOESY sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
163D H(C)CH-TOCSY aromatic, sparse0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
173D (H)CCH-TOCSY aromatic0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
182D CT 1H-13C HSQC0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
192D CT 1H-13C HSQC aromatic0.5 mM [U-13C; U-15N] HP0495, 10 mM TRIS, 300 mM sodium chloride, 1 mM benzamidine, 10 mM DTT, 0.01 % sodium azide100% D2O3007ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE500
2BrukerAVANCE600
3BrukerAVANCE800
4VarianINOVA500
NMR Refinement
MethodDetailsSoftware
molecular dynamicswater refinement with CNSCNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsBoth 4D experiments were collected as 2D projection planes and processed with PR experiments marked "sparse" were collected with non-uniform sampling and processed with MDD
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read
2structure solutionCYANA2.1Guntert, Mumenthaler and Wuthrich
3peak pickingSparkyGoddard
4dihedral angle constraints predictionTALOSCornilescu, Delaglio and Bax
5chemical shift and noe assignmentABACUSA. Lemak, A. Grishaev, M. Llinas, CH Arrowsmith
6processing of non-uniformly sampled dataMDD/MDDguiA. Gutmanas, CH Arrowsmith, I Ibraghimov, V Yu Orekhov
7processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8processing of projection-reconstruction spectraPRM Karra, CH Arrowsmith