Solution NMR structure of uncharacterized protein Q5E7H1 from Vibrio fischeri. Northeast Structural Genomics target VfR117
Northeast Structural Genomics Consortium (NESG)
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
MALIMTQQNNPLHGITLQKLLTELVEHYGWEELSYMVNINCFKKDPSIKSSLKFLRKTDWARERVENIYLKLQRHKERNQ LEHHHHHH
Northeast Structural Genomics Consortium
THE 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.
2D 1H-13C HSQC stereospecific Leu/Val methyl
THE 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.
0.95 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 azide, 95% H2O/5% D2O
1.08 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 azide, 95% H2O/5% D2O
Zimmerman, Moseley, Kulikowski and Montelione
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
Brunger, Adams, Clore, Gros, Nilges and Read
solution NMR structure, alpha helical protein, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG