NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

image	mrblock_id	pdb_id	bmrb_id	cing	in_dress	stage	program	type
	2021	1bbn	4094	cing	dress	1-original	MR format	comment

*HEADER   CYTOKINE                                01-MAY-92   1BBN    
*COMPND   INTERLEUKIN 4 (NMR, MINIMIZED AVERAGE STRUCTURE)            
*SOURCE   HUMAN (HOMO SAPIENS) RECOMBINANT FORM EXPRESSED IN YEAST    
*SOURCE  2 (SACCHAROMYCES CEREVISIAE)                                 
*AUTHOR   G.M.CLORE,B.POWERS,D.S.GARRETT,A.M.GRONENBORN               
*REVDAT  1   31-OCT-93 1BBN    0                                      

REMARK Experimental NMR restraints used for the three-dimensional structure 
REMARK determination of recombinant human interleukin-4
REMARK 
REMARK
REMARK Authors: G.M. Clore, B. Powers, D.S. Garrett and A.M. Gronenborn
REMARK
REMARK References
REMARK
REMARK 1.  R. Powers, D.S. Garrett, C.J. March, E.A. Frieden, A.M. Gronenborn
REMARK     and G.M. Clore (1992) Three dimensional solution structure of 
REMARK     human interleukin-4 by multidimensional heteronuclear magnetic 
REMARK     resonance spectroscopy. Science in press
REMARK
REMARK 2.  R. Powers, D.S. Garrett, C.J. March, E.A. Frieden, A.M. Gronenborn
REMARK     and G.M. Clore (1992) 1H, 15N, 13C and 13CO assignments of human
REMARK     interleukin-4 using three-dimensional double- and triple-resonance
REMARK     hetronuclear magnetic resonance spectroscopy. Biochemistry 31, issue
REMARK     18, in press
REMARK
REMARK 3.  D.S. Garrett, R. Powers, C.J. March, E.A. Frieden, G.M. Clore
REMARK     and A.M. Gronenborn (1992) Determination of the secondary structure
REMARK     and folding topology of human interleukin-4 using three-dimensional
REMARK     heteronuclear magnetic resonance spectroscopy. Biochemistry 31,
REMARK     issue 18, in press
REMARK
REMARK    All the coordinates
REMARK    are included here as a separate file: il4_brookhaven.pdb
REMARK 
REMARK     The numbering scheme in this structure includes the four-residue
REMARK     sequence Glu-Ala-Glu-Ala at the N-terminus of the recombinant
REMARK     protein which is not part of the natural human IL-4; the natural
REMARK     IL-4 sequence therefore starts at residue 5.
REMARK
REMARK    Details of the structure determination and all structural
REMARK    statistics are given in ref. 1 (i.e. agreement with experimental
REMARK    restraints, deviations from ideality for bond lengths, angles,
REMARK    planes and chirality, non-bonded contacts, atomic rms differences
REMARK    between the calculated structures).
REMARK    The structures are based on 823 interproton distance restraints
REMARK    derived from NOE measurements; 98 hydrogen-bonding distance
REMARK    restraints for 49 hydrogen-bonds identified on the basis of the
REMARK    NOE and amide proton exchange data, as well as the initial structure
REMARK    calculations; and 101 phi and 82 psi backbone torsion angle 
REMARK    restraints derived from oupling constants, NOE data, and 13C
REMARK    secondary chemical shifts. 
REMARK
REMARK    The method used to determine the structures
REMARK    is the hybrid metric matrix distance geometry-dynamical simulated
REMARK    annealing method  [Nilges, M., Clore, G.M. & Gronenborn, A.M.
REMARK    FEBS Lett. 229, 317-324 (1988)].
REMARK
REMARK
REMARK
REMARK    The NOE restraints are given in (A) and the torsion angle restraints
REMARK    in (B).
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.

Contact the webmaster for help, if required. Thursday, May 2, 2024 10:57:44 AM GMT (wattos1)