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PDBsum entry 1j4z
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Contents |
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* Residue conservation analysis
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Obsolete entry |
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PDB id:
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Chaperone
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Title:
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Structural and mechanistic basis for allostery in the bacterial chaperonin groel; see remark 400
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Structure:
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Groel protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Synonym: 60 kda chaperonin, protein cpn60, groel protein, ams. Engineered: yes. Mutation: yes
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Source:
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Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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40mer (from
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Resolution:
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3.52Å
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R-factor:
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0.291
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R-free:
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0.298
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Authors:
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J.Wang
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Key ref:
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G.M.Clore
and
C.A.Bewley
(2002).
Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings.
J Magn Reson,
154,
329-335.
PubMed id:
DOI:
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Date:
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02-Jan-02
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Release date:
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18-Nov-03
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PROCHECK
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Headers
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References
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P0A6F5
(CH60_ECOLI) -
60 kDa chaperonin from Escherichia coli (strain K12)
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Seq:
Struc:
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548 a.a.
525 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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J Magn Reson
154:329-335
(2002)
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PubMed id:
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Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings.
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G.M.Clore,
C.A.Bewley.
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ABSTRACT
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A simple and robust method for determining the relative orientations of
covalently linked protein domains using conjoined rigid body/torsion angle
dynamics simulated annealing on the basis of residual dipolar couplings is
presented. In this approach each domain is treated as a rigid body and the
relevant degrees of conformational freedom are restricted to the backbone
torsion angles (phi, psi) of the linker between the domains. By this means
translational information afforded by the presence of an intact linker is
preserved. We illustrate this approach using the domain-swapped dimer of the
HIV-inactivating protein cyanovirin-N as an example.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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G.A.Bermejo,
M.P.Strub,
C.Ho,
and
N.Tjandra
(2010).
Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein.
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Biochemistry,
49,
1893-1902.
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G.A.Bermejo,
M.P.Strub,
C.Ho,
and
N.Tjandra
(2009).
Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space.
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J Am Chem Soc,
131,
9532-9537.
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A.Grishaev,
J.Ying,
M.D.Canny,
A.Pardi,
and
A.Bax
(2008).
Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.
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J Biomol NMR,
42,
99.
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PDB code:
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G.M.Clore
(2008).
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement.
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Mol Biosyst,
4,
1058-1069.
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M.Bryson,
F.Tian,
J.H.Prestegard,
and
H.Valafar
(2008).
REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data.
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J Magn Reson,
191,
322-334.
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R.Fromme,
Z.Katiliene,
P.Fromme,
and
G.Ghirlanda
(2008).
Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution.
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Protein Sci,
17,
939-944.
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PDB code:
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S.Rumpel,
R.Lakshmi,
S.Becker,
and
M.Zweckstetter
(2008).
Assignment-free solution NMR method reveals CesT as an unswapped homodimer.
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Protein Sci,
17,
2015-2019.
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X.Miao,
R.Mukhopadhyay,
and
H.Valafar
(2008).
Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application.
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J Magn Reson,
194,
202-211.
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C.Tang,
C.D.Schwieters,
and
G.M.Clore
(2007).
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR.
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Nature,
449,
1078-1082.
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PDB code:
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K.McFadden,
S.Cocklin,
H.Gopi,
S.Baxter,
S.Ajith,
N.Mahmood,
R.Shattock,
and
I.Chaiken
(2007).
A recombinant allosteric lectin antagonist of HIV-1 envelope gp120 interactions.
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Proteins,
67,
617-629.
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Y.Ryabov,
and
D.Fushman
(2007).
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
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J Am Chem Soc,
129,
7894-7902.
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PDB codes:
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R.E.Gillilan,
and
R.H.Lilien
(2004).
Optimization and dynamics of protein-protein complexes using B-splines.
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J Comput Chem,
25,
1630-1646.
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R.S.Lipsitz,
and
N.Tjandra
(2004).
Residual dipolar couplings in NMR structure analysis.
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Annu Rev Biophys Biomol Struct,
33,
387-413.
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J.A.Lukin,
G.Kontaxis,
V.Simplaceanu,
Y.Yuan,
A.Bax,
and
C.Ho
(2003).
Quaternary structure of hemoglobin in solution.
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Proc Natl Acad Sci U S A,
100,
517-520.
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A.Dvoretsky,
E.M.Abusamhadneh,
J.W.Howarth,
and
P.R.Rosevear
(2002).
Solution structure of calcium-saturated cardiac troponin C bound to cardiac troponin I.
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J Biol Chem,
277,
38565-38570.
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PDB code:
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G.Cornilescu,
B.R.Lee,
C.C.Cornilescu,
G.Wang,
A.Peterkofsky,
and
G.M.Clore
(2002).
Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.
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J Biol Chem,
277,
42289-42298.
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PDB code:
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G.M.Clore,
and
C.D.Schwieters
(2002).
Theoretical and computational advances in biomolecular NMR spectroscopy.
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Curr Opin Struct Biol,
12,
146-153.
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I.Botos,
B.R.O'Keefe,
S.R.Shenoy,
L.K.Cartner,
D.M.Ratner,
P.H.Seeberger,
M.R.Boyd,
and
A.Wlodawer
(2002).
Structures of the complexes of a potent anti-HIV protein cyanovirin-N and high mannose oligosaccharides.
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J Biol Chem,
277,
34336-34342.
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PDB codes:
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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
code is
shown on the right.
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Links
