2JT1 | pdb_00002jt1

Solution NMR structure of PefI (Plasmid-Encoded Fimbriae Regulatory) protein from Salmonella typhimurium. Northeast Structural Genomics target StR82


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
22D 1H-13C HSQC0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
33D HNCO0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
43D HN(CA)CO0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
53D HNCACB0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
63D HN(COCA)CB0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
73D HBHA(CO)NH0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
83D HCCH-COSY0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
93D CCH-TOCSY0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
103D simultaneous CN-NOESY0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
113D HNHA0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
123D 1H-13C NOESY aromatic0.72 mM [U-100% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
132D 1H-13C HSQC stereospecific LEU/VAL methyl0.46 mM [U-5% 13C; U-100% 15N] Str82, 20 mM ammonium acetate, 450 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide95% H2O/5% D2O4505.5ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE800
2BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
simulated annealingTHE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1155 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 92 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (19.1 CONSTRAINTS PER RESIDUE, 4.5 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 71 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.TopSpin
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
DetailsTHE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.8%, SIDE CHAIN, 95.8%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 71, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 5-19,23-57,66-69: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 95.9%, ADDITIONALLY ALLOWED, 4.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.16/0.94, ALL, 0.11/0.65. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 21.29/-2.13. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-71): RECALL, 0.983, PRECISION, 0.930, F-MEASURE, 0.956, DP-SCORE, 0.789. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-4,20-22,58-65,70-71.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpin1.3Bruker Biospin
2chemical shift assignmentAutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelione
3structure solutionCYANA2.1Guntert, Mumenthaler and Wuthrich
4processingNMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5refinementCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read
6data analysisAutoStructure2.1.1Huang, Tejero, Powers and Montelione
7structure validationPSVS1.3Bhattacharya and Montelione
8pdb analysisPdbStat5.0Tejero and Montelione
9structure validationProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th
10structure validationMolProbityRichardson
11structure visualizationMOLMOL2K-2Koradi, Billeter and Wuthrich
12data analysisSparky3.110Goddard