NMR Restraints Grid |
Result table
image | mrblock_id | pdb_id | bmrb_id | cing | in_recoord | stage | program | type |
9130 | 1ner | 287 | cing | recoord | 1-original | MR format | comment |
*HEADER DNA-BINDING PROTEIN 24-AUG-95 1NER *TITLE SOLUTION STRUCTURE OF THE MU NER PROTEIN BY MULTIDIMENSIONAL *TITLE 2 NMR *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: DNA-BINDING PROTEIN NER; *COMPND 3 CHAIN: NULL *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE MU *EXPDTA NMR, 30 STRUCTURES *AUTHOR G.M.CLORE,T.E.STRZELECKA,A.M.GRONENBORN *REVDAT 1 07-DEC-95 1NER 0 REMARK Experimental restraints used for the solution structure determination REMARK of the Mu Ner Protein by multidimensional NMR REMARK REMARK Authors: G.M. Clore, T.E. Strzelecka and A.M. Gronenborn REMARK Laboratory of Chemical Physics, Bldg 5, Rm 132 REMARK NIDDK, National Institutes of Health REMARK Bethesda, MD 20892 REMARK Tel: (301) 496 0782; FAX (301) 496 0825; REMARK e-mail: clore@vger.niddk.nih.gov REMARK REMARK References: REMARK Strzelecka, T.E., Clore, G.M. & Gronenborn, A.M. (1995) REMARK The solution structure of the Mu Ner Protein reveals a helix-turn- REMARK helix DNA recognition motif. Structure in press. REMARK REMARK Related references: REMARK Gronenborn, A.M., Wingfield, P.T. & Clore, G.M. (1989) REMARK Determination of the secondary structure of the DNA binding protein REMARK Ner from phage Mu using 1H homonuclear and 15N-1H heteronuclear REMARK NMR spectroscopy. Biochemistry 28, 5081-5089. REMARK REMARK The 3D structure of the Mu Ner protein by REMARK multi-dimensional heteronuclear NMR REMARK is based on 1546 experimental restraints comprising the following: REMARK 944 interproton distance restraints [251 sequential; 202 short REMARK range (1<|i-j|<=5; 157 long range (|i-j|>5); and 334 intraresidue]; REMARK 40 distance restraints for 20 backbone hydrogen bonds; REMARK 89 torsion angle restraints 56 phi, 27 ch1 and 6 chi2); REMARK 46 3 bond HN-Ha coupling constants; 140 secondary 13C shifts REMARK (72 Ca and 68 Cb); 287 1H chemical shifts (74 Ha, 39 methyl REMARK and 174 other, with no exchangeable proton shifts). REMARK REMARK REMARK The structure was determined by simulated annealing [Nilges, REMARK Clore & Gronenborn (1988) FEBS Lett. 229, 317-324] using the REMARK program XPLOR (Brunger) modified to incorporate coupling constant REMARK [Garrett et al. & Clore (1994) J. Magn. Reson. B104, 99-103], REMARK carbon chemical shift [Kuszewski, Qin, Gronenborn & Clore (1995) REMARK J. Magn. Reson. B106, 92-96] and proton chemical shift REMARK [Kuszewski, Gronenborn & Clore (1995) J. Magn. Reson. B107, 293-297] REMARK restraints. REMARK The structures have been provided in a separate files: REMARK ner_brookhaven.pdb REMARK REMARK The NOE restraints are given in (A), the torsion angle restraints REMARK in (B), the coupling constant restraints in (C), the REMARK carbon chemical shift restraints in (D), the 1H chemical shift REMARK restraints in (E). REMARK The complete set of 1H, 15N and 13C assignments is given in F. REMARK REMARK A. NOE interproton distance restraints The restraints are represented by square-well potentials with the upper (u) and lower (l) limits given by u=i+k and l=i-j where the numbers are entered in the order i,j,k. [Clore et al. (1986) EMBO J. 5, 2729-2735] The NOEs are classified into three distance ranges corresponding to strong, medium and weak NOEs. These are 1.8-2.7 A, 1.8-3.3 A and 1.8-5.0 A, respectively. In addition, an extra 0.5 A is added to the upper limits of distances involving methyl protons [Clore et al. (1983) Biochemistry 26, 8012-8023; Wagner et al. (1987) J. Mol. Biol. 196, 611-640]. The atom notation follows standard PDB format. The # indicates a single wild card, and the * a full wild card. e.g. For Leu, HD* representes all the methyl protons; for a normal methylene beta proton, HB# represents the two protons. In these cases, the distances are calculated as sigma-1/6 sums Note that the hard sphere van der Waals repulsion term ensures that the minimum lower limit for all distances is the sum of the relevant hard sphere atom radii. B. Torsion angle restraints The torsion angle restraints are derived from coupling constant and NOE data using the conformational grid search program STEREOSEARCH [Nilges, M., Clore, G.M. & Gronenborn, A.M. (1990) Biopolymers 29, 813-822]. They are represented by a square well potential [Clore et al. (1986) EMBO J. 5, 2729-2735]. The upper and lower limits are given by i+j and i-j respectively, where the numbers are entered in the order x,i,j,m. x is the force constant and m the exponent used to compute the torsion angle restraints target function. C. Three-bond HN-HA coupling constant restraints. The value of the coupling constant is given by the first number, and the second number has no meaning. D. Ca and Cb carbon chemical shift restraints: the Ca shift is given by the first number and the Cb one by the second. E. 1H chemical shift restraints F. Complete list of 1H, 15N and 13C assignments A. interproton distance restraints
Contact the webmaster for help, if required. Tuesday, May 14, 2024 3:54:35 PM GMT (wattos1)