 |
PDBsum entry 1ccm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Plant seed protein
|
PDB id
|
|
|
|
1ccm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Proteins
15:385-400
(1993)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
|
|
A.M.Bonvin,
J.A.Rullmann,
R.M.Lamerichs,
R.Boelens,
R.Kaptein.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The structure in solution of crambin, a small protein of 46 residues, has been
determined from 2D NMR data using an iterative relaxation matrix approach (IRMA)
together with distance geometry, distance bound driven dynamics, molecular
dynamics, and energy minimization. A new protocol based on an "ensemble"
approach is proposed and compared to the more standard initial rate analysis
approach and a "single structure" relaxation matrix approach. The effects of
fast local motions are included and R-factor calculations are performed on NOE
build-ups to describe the quality of agreement between theory and experiment. A
new method for stereospecific assignment of prochiral groups, based on a
comparison of theoretical and experimental NOE intensities, has been applied.
The solution structure of crambin could be determined with a precision (rmsd
from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy
atoms and is largely similar to the crystal structure with a small difference
observed in the position of the side chain of Tyr-29 which is determined in
solution by both J-coupling and NOE data. Regions of higher structural
variability (suggesting higher mobility) are found in the solution structure, in
particular for the loop between the two helices (Gly-20 to Pro-22).
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
Y.Cote,
P.Senet,
P.Delarue,
G.G.Maisuradze,
and
H.A.Scheraga
(2010).
Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.
|
| |
Proc Natl Acad Sci U S A,
107,
19844-19849.
|
|
|
|
|
|
|
L.Liu,
L.M.Koharudin,
A.M.Gronenborn,
and
I.Bahar
(2009).
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations.
|
| |
Proteins,
77,
927-939.
|
|
|
|
|
|
|
P.R.Markwick,
G.Bouvignies,
L.Salmon,
J.A.McCammon,
M.Nilges,
and
M.Blackledge
(2009).
Toward a unified representation of protein structural dynamics in solution.
|
| |
J Am Chem Soc,
131,
16968-16975.
|
|
|
|
|
|
|
P.Senet,
G.G.Maisuradze,
C.Foulie,
P.Delarue,
and
H.A.Scheraga
(2008).
How main-chains of proteins explore the free-energy landscape in native states.
|
| |
Proc Natl Acad Sci U S A,
105,
19708-19713.
|
|
|
|
|
|
|
G.Bouvignies,
P.R.Markwick,
and
M.Blackledge
(2007).
Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.
|
| |
Chemphyschem,
8,
1901-1909.
|
|
|
|
|
|
|
A.Kitao,
and
G.Wagner
(2006).
Amplitudes and directions of internal protein motions from a JAM analysis of 15N relaxation data.
|
| |
Magn Reson Chem,
44,
S130-S142.
|
|
|
|
|
|
|
H.C.Ahn,
N.Juranić,
S.Macura,
and
J.L.Markley
(2006).
Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface.
|
| |
J Am Chem Soc,
128,
4398-4404.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Pristovsek,
and
L.Franzoni
(2006).
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data.
|
| |
J Comput Chem,
27,
791-797.
|
|
|
|
|
|
|
K.Lindorff-Larsen,
R.B.Best,
M.A.Depristo,
C.M.Dobson,
and
M.Vendruscolo
(2005).
Simultaneous determination of protein structure and dynamics.
|
| |
Nature,
433,
128-132.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.L.Ulfers,
J.L.McMurry,
A.Miller,
L.Wang,
D.A.Kendall,
and
D.F.Mierke
(2002).
Cannabinoid receptor-G protein interactions: G(alphai1)-bound structures of IC3 and a mutant with altered G protein specificity.
|
| |
Protein Sci,
11,
2526-2531.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
F.Fraternali,
P.Amodeo,
G.Musco,
M.Nilges,
and
A.Pastore
(1999).
Exploring protein interiors: the role of a buried histidine in the KH module fold.
|
| |
Proteins,
34,
484-496.
|
|
|
|
|
|
|
L.S.Caves,
J.D.Evanseck,
and
M.Karplus
(1998).
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.
|
| |
Protein Sci,
7,
649-666.
|
|
|
|
|
|
|
S.Singh,
P.K.Patel,
and
R.V.Hosur
(1997).
Structural polymorphism and dynamism in the DNA segment GATCTTCCCCCCGGAA: NMR investigations of hairpin, dumbbell, nicked duplex, parallel strands, and i-motif.
|
| |
Biochemistry,
36,
13214-13222.
|
|
|
|
|
|
|
T.N.Jaishree,
V.Ramakrishnan,
and
S.W.White
(1996).
Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.
|
| |
Biochemistry,
35,
2845-2853.
|
|
|
|
|
|
|
R.T.Clowes,
A.Crawford,
A.R.Raine,
B.O.Smith,
and
E.D.Laue
(1995).
Improved methods for structural studies of proteins using nuclear magnetic resonance spectroscopy.
|
| |
Curr Opin Biotechnol,
6,
81-88.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
