2JS7

Solution NMR structure of human myeloid differentiation primary response (MyD88). Northeast Structural Genomics target HR2869A


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
22D 1H-13C HSQC0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
33D HNCACB0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
43D HNCO0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
53D HNCA0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
63D HN(COCA)CB0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
73D HN(CO)CA0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
83D HN(CA)CO0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
93D HBHA(CO)NH0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
103D 1H-13C NOESY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
113D 1H-15N NOESY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
123D HCCH-COSY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
133D HCCH-TOCSY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
143D CCH-TOCSY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
152D 1H-13C HSQC stereospecific VL0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
163D 1H-13C NOESY0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile100% D2O5.0ambient303
172D 1H-13C HSQC0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile100% D2O5.0ambient303
18H/D exch0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile100% D2O5.0ambient303
19HETnoe0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
20T1/T20.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile95% H2O/5% D2O5.0ambient303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
simulated annealingMONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA AND AUTOSTRUCTURE IN A CONSENSUS APPROACH. SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED WITH CYANA, LOWEST ENERGY SELECTED IN AUTOSTRUCTURE USING NIH-XPLOR FOR SIMULATEED ANNEALING MD. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.36%, SIDECHAIN 95.8%, AROMATIC (SC) 93.1%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2795 NOE. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.35 A (1MODEL). 16 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELIX (28-39, 68-71, 81-85, 87-99, 103-106, 141-150), BETA-STRAND (48-49, 17-22, 72-78, 108-112, 130-131) [S(PHI)+ (PSI)] > 1.8. RMSD 0.6 BB, 0.9 ALL HEAVY ATOMS. RAMACHANDRAN: 88.0% MOST FAV, 11.4% ADDTL ALLOW, 0.5 GENEROUS ALLOW, 0.1% DISALLOW. PROCHECK (PSI-PHI): -0.22/-0.55 (RAW/Z), PROCHECK (ALL): -0.15/-0.89 (RAW/Z), MOLPROBITY CLASH: 27.22/-3.15 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.934, PRECISION: 0.892, F-MEASURE: 0.913, DP-SCORE: 0.721.CYANA
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
1structure solutionCYANA2.1Guntert, Mumenthaler and Wuthrich
2structure solutionAutoStructure2.1.1Huang, Tejero, Powers and Montelione
3chemical shift assignmentAutoAssign1.14Zimmerman, Moseley, Kulikowski and Montelione
4data analysisSparky2.110Goddard
5processingNMRPipe2005Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6collectionTopSpin1.3Bruker Biospin
7visualizationMOLMOL2K.2Koradi, Billeter and Wuthrich
8validationPSVS1.3Bhattacharya and Montelione
9validationProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th
10refinementCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read
11refinementX-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clore
12validationMolProbityRichardson