2JVW

Solution NMR structure of uncharacterized protein Q5E7H1 from Vibrio fischeri. Northeast Structural Genomics target VfR117


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
22D 1H-13C HSQC0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
33D HNCO0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
43D HN(CA)CO0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
53D HN(COCA)CB0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
63D HNCACB0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
73D HBHA(CO)NH0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
83D HCCH-COSY0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
93D HCCH-TOCSY0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
103D CCH-TOCSY0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
113D CCH-TOCSY aromatic0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
123D simultaneous CN-NOESY0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
133D HNHA0.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
142D 1H-13C HSQC stereospecific Leu/Val methyl1.08 mM [U-5% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide95% H2O/5% D2O0.14.5ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE800
2BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
simulated annealingTHE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND CONSTRAINTS (19.2 CONSTRAINTS PER RESIDUE, 3.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 82 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, 98.8%, SIDE CHAIN, 95.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 82, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 15-37,42-43,46-75: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.17/0.98, ALL, 0.19/1.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.65/-0.99. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-82): RECALL, 0.989, PRECISION, 0.945, F-MEASURE, 0.967, DP-SCORE, 0.810. (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]: 1-14,38-41,44-45,76-82.
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
5rpf analysisAutoStructure2.1.1Huang, Tejero, Powers and Montelione
6structure validationPSVS1.3Bhattacharya and Montelione
7pdb analysisPdbStat5.0Tejero and Montelione
8data analysisSparky3.110Goddard
9peak pickingSparky3.110Goddard
10refinementCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read