NMR Restraints Grid
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NMR Restraints Grid |
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Result table
| image | mrblock_id | pdb_id | cing | stage | program | type |
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11959 |
1saf   |
cing | 1-original | MR format | comment |
*HEADER ANTI-ONCOGENE 12-MAR-95 1SAF *TITLE HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE *TITLE 2 OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR *TITLE 3 (SAD STRUCTURES) *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: TUMOR SUPPRESSOR P53; *COMPND 3 CHAIN: A, B, C, D; *COMPND 4 DOMAIN: OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360; *COMPND 5 OTHER_DETAILS: SAD STRUCTURES 1 - 26 *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; *SOURCE 3 ORGANISM_COMMON: HUMAN *EXPDTA NMR, 26 STRUCTURES *AUTHOR G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN *REVDAT 1 15-OCT-95 1SAF 0 REMARK Experimental NMR restraints for the REMARK high resolution solution NMR structure determination of the REMARK Oligomerization Domain of p53 by Multi-Dimensional NMR REMARK Restraints used for p53_radius_c_brookhaven.pdb and p53_radius_d_brookhaven.pdb REMARK coordinates. REMARK REMARK Authors: G.M. Clore, J.G. Omichinski 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 G.M. Clore, J. Ernst, R. Clubb, J.G. Omichinski, W.M. Poindexter REMARK Kennedy, K. Sakaguchi, E. Appella, and A.M. Gronenborn (1995) REMARK Refined solution structur of the oligomerization domain of the REMARK tumour suppressor p53. NAture Structural Biology, 2, number 4 REMARK April issue. REMARK REMARK Related references: REMARK 1. G.M. Clore, J.G. Omichinski, K. Sakaguchi, N. Zambrano, H. Sakamoto, REMARK E. Appella and A.M. Gronenborn High resolution structure of the REMARK oligomerization domain of p53 by multidimensional NMR. REMARK Science 265, 386-391 (1994) REMARK REMARK 2. G.M. Clore, J.G. Omichinski, K. Sakaguchi, N. Zambrano, H. Sakamoto, REMARK E. Appella and A.M. Gronenborn Interhelical angles in the solution REMARK structure of the oligomerization domain of the tumour suppressor REMARK p53. Science in press (scheduled for publication in March 95). REMARK REMARK REMARK The 3D structure of the oligomerization domain (residues 319-360) REMARK of p53 by multid-dimensional heteronuclear-edited and -filtered REMARK NMR is based on 4472 experimental restraints comprising the following REMARK intra- and inter-subunit restraints: REMARK (a) intrasubunit: 852 sequential (|i-j|=1), 712 medium REMARK range (1 < |i-j| >=5) and 76 long range (|i-j| >5) interresidues and REMARK 740 intraresidue approximate interproton distance restraints, 136 REMARK distance restraints for 68 hydrogen bonds, 284 torsion angle REMARK (144 phi, 104 chi1 and 36 chi2) restraints, and 144 three-bond REMARK HN-Ha coupling constant restraints. REMARK (b) intersubunit: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C approximate REMARK interproton distance restraints, and 24 distance restraints for REMARK 12 hydrogen bonds involving the A-C/B-D subunits. REMARK In addition, there are a total of 38 Calpha and 38 Cb chemical REMARK shift restraints per subunit that have been incorporated REMARK into the refinement [J. Kuszweski, J. Qin, A.M. Gronenborn REMARK and G.M. Clore, J. Magn Reson. Ser in press (1994)] REMARK REMARK REMARK REMARK The structures have been provided in two separate files: REMARK p53_radius_c_brookhaven.pdb and p53_radius_d_brookhaven.pdb REMARK REMARK The NOE restraints are given in (A), the torsion angle restraints REMARK in (B), the coupling constant restraints in (C), and the REMARK chemical shift restraints in (D). REMARK REMARK The complete set of 1H, 15N and 13C assignments is given in 1OLH_MR. 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. Appropriate corrections to the upper limits for distances involving methyl, methylene and Tyr and Phe aromatic ring protons, to account for centre averaging, are carried out as described by Wuthrich et al. [J. Mol. Biol. 169, 949-961 (1983)]. 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 centreaverages. 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. A. interproton distance restraints
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