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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38901 |
1saf   |
cing | 2-parsed | STAR | comment |
data_1saf_MR_file_constraints
save_Conversion_project
_Study_list.Sf_category study_list
_Study_list.Entry_ID parsed_1saf
_Study_list.ID 1
loop_
_Study.ID
_Study.Name
_Study.Type
_Study.Details
_Study.Entry_ID
_Study.Study_list_ID
1 "Conversion project" NMR . parsed_1saf 1
stop_
save_
save_entry_information
_Entry.Sf_category entry_information
_Entry.ID parsed_1saf
_Entry.Title "Original constraint list(s)"
_Entry.Version_type original
_Entry.Submission_date .
_Entry.Accession_date .
_Entry.Last_release_date .
_Entry.Original_release_date .
_Entry.Origination .
_Entry.NMR_STAR_version 3.1
_Entry.Original_NMR_STAR_version .
_Entry.Experimental_method NMR
_Entry.Experimental_method_subtype .
loop_
_Related_entries.Database_name
_Related_entries.Database_accession_code
_Related_entries.Relationship
_Related_entries.Entry_ID
PDB 1saf "Master copy" parsed_1saf
stop_
save_
save_global_Org_file_characteristics
_Constraint_stat_list.Sf_category constraint_statistics
_Constraint_stat_list.Entry_ID parsed_1saf
_Constraint_stat_list.ID 1
loop_
_Constraint_file.ID
_Constraint_file.Constraint_filename
_Constraint_file.Software_ID
_Constraint_file.Software_label
_Constraint_file.Software_name
_Constraint_file.Block_ID
_Constraint_file.Constraint_type
_Constraint_file.Constraint_subtype
_Constraint_file.Constraint_subsubtype
_Constraint_file.Constraint_number
_Constraint_file.Entry_ID
_Constraint_file.Constraint_stat_list_ID
1 1saf.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 2 distance NOE simple 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 3 distance "hydrogen bond" simple 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 4 distance NOE simple 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 5 distance "hydrogen bond" simple 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 6 distance "hydrogen bond" simple 0 parsed_1saf 1
1 1saf.mr . . n/a 7 comment "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 8 "dihedral angle" "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . n/a 9 comment "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 10 "coupling constant" "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . n/a 11 comment "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . XPLOR/CNS 12 "chemical shift" "Not applicable" "Not applicable" 0 parsed_1saf 1
1 1saf.mr . . "MR format" 13 "nomenclature mapping" "Not applicable" "Not applicable" 0 parsed_1saf 1
stop_
save_
save_MR_file_comment_1
_Org_constr_file_comment.Sf_category org_constr_file_comment
_Org_constr_file_comment.Entry_ID parsed_1saf
_Org_constr_file_comment.ID 1
_Org_constr_file_comment.Constraint_file_ID 1
_Org_constr_file_comment.Block_ID 1
_Org_constr_file_comment.Details "Generated by Wattos"
_Org_constr_file_comment.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 centre
averages.
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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save_
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