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PDBsum entry 1ycc
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Electron transport (cytochrome)
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PDB id
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1ycc
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Contents |
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* Residue conservation analysis
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J Mol Biol
214:527-555
(1990)
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PubMed id:
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High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c.
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G.V.Louie,
G.D.Brayer.
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ABSTRACT
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The structure of yeast iso-1-cytochrome c has been refined against X-ray
diffraction data to a nominal resolution of 1.23 A. The atomic model contains
893 protein atoms, as well as 116 water molecules and one sulfate anion. Also
included in the refinement are 886 hydrogen atoms belonging to the protein
molecule. The crystallographic R-factor is 0.192 for the 12,513 reflections with
F greater than or equal to 3 sigma (F) in the resolution range 6.0 to 1.23 A.
Co-ordinate accuracy is estimated to be better than 0.18 A. The iso-1-cytochrome
c molecule has the typical cytochrome c fold, with the polypeptide chain
organized into a series of alpha-helices and reverse turns that serve to envelop
the heme prosthetic group in a hydrophobic pocket. Inspection of the
conformations of helices in the molecule shows that the local environments of
the helices, in particular the presence of intrahelical threonine residues,
cause distortions from ideal alpha-helical geometry. Analysis of the internal
mobility of iso-1-cytochrome c, based on refined crystallographic temperature
factors, shows that the most rigid parts of the molecule are those that are
closely associated with the heme group. The degree of saturation of
hydrogen-bonding potential is high, with 90% of all polar atoms found to
participate in hydrogen bonding. The geometry of intramolecular hydrogen bonds
is typical of that observed in other high-resolution protein structures. The 116
water molecules present in the model represent about 41% of those expected to be
present in the asymmetric unit. The majority of the water molecules are
organized into a small number of hydrogen-bonding networks that are anchored to
the protein surface. Comparison of the structure of yeast iso-1-cytochrome c
with those of tuna and rice cytochromes c shows that these three molecules have
very high structural similarity, with the atomic packing in the heme crevice
region being particularly highly conserved. Large conformational differences
that are observed between these cytochromes c can be explained by amino acid
substitutions. Additional subtle differences in the positioning of the
side-chains of several highly conserved residues are also observed and occur due
to unique features in the local environments of each cytochrome c
molecule.(ABSTRACT TRUNCATED AT 400 WORDS)
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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.J.Pound,
A.A.Pletnev,
X.Fang,
and
E.V.Pletneva
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A small fluorophore reporter of protein conformation and redox state.
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Chem Commun (Camb),
47,
5714-5716.
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P.B.Crowley,
E.Chow,
and
T.Papkovskaia
(2011).
Protein interactions in the Escherichia coli cytosol: an impediment to in-cell NMR spectroscopy.
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Chembiochem,
12,
1043-1048.
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F.Sinibaldi,
B.D.Howes,
M.C.Piro,
F.Polticelli,
C.Bombelli,
T.Ferri,
M.Coletta,
G.Smulevich,
and
R.Santucci
(2010).
Extended cardiolipin anchorage to cytochrome c: a model for protein-mitochondrial membrane binding.
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J Biol Inorg Chem,
15,
689-700.
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L.J.Smith,
A.Kahraman,
and
J.M.Thornton
(2010).
Heme proteins--diversity in structural characteristics, function, and folding.
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Proteins,
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Protein thin film machines.
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Nanoscale,
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Phosphorylation by Nek1 regulates opening and closing of voltage dependent anion channel 1.
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Biochem Biophys Res Commun,
394,
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M.E.Aubin-Tam,
W.Hwang,
and
K.Hamad-Schifferli
(2009).
Site-directed nanoparticle labeling of cytochrome c.
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| |
Proc Natl Acad Sci U S A,
106,
4095-4100.
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X.Xu,
P.H.Keizers,
W.Reinle,
F.Hannemann,
R.Bernhardt,
and
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Intermolecular dynamics studied by paramagnetic tagging.
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J Biomol NMR,
43,
247-254.
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Y.Zhang,
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J.E.Straub,
J.Zhao,
W.Sturhahn,
E.E.Alp,
and
J.T.Sage
(2008).
Resilience of the iron environment in heme proteins.
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Biophys J,
95,
5874-5889.
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P.B.Crowley,
K.Brett,
and
J.Muldoon
(2008).
NMR spectroscopy reveals cytochrome c-poly(ethylene glycol) interactions.
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Chembiochem,
9,
685-688.
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P.B.Crowley,
P.Ganji,
and
H.Ibrahim
(2008).
Protein surface recognition: structural characterisation of cytochrome c-porphyrin complexes.
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Chembiochem,
9,
1029-1033.
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G.Silkstone,
A.Jasaitis,
M.T.Wilson,
and
M.H.Vos
(2007).
Ligand dynamics in an electron transfer protein. Picosecond geminate recombination of carbon monoxide to heme in mutant forms of cytochrome c.
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J Biol Chem,
282,
1638-1649.
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L.Andolfi,
P.Caroppi,
A.R.Bizzarri,
M.C.Piro,
F.Sinibaldi,
T.Ferri,
F.Polticelli,
S.Cannistraro,
and
R.Santucci
(2007).
Nanoscopic and redox characterization of engineered horse cytochrome C chemisorbed on a bare gold electrode.
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Protein J,
26,
271-279.
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M.S.Li
(2007).
Secondary structure, mechanical stability, and location of transition state of proteins.
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Biophys J,
93,
2644-2654.
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C.A.Bottoms,
T.A.White,
and
J.J.Tanner
(2006).
Exploring structurally conserved solvent sites in protein families.
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Proteins,
64,
404-421.
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F.Sinibaldi,
B.D.Howes,
M.C.Piro,
P.Caroppi,
G.Mei,
F.Ascoli,
G.Smulevich,
and
R.Santucci
(2006).
Insights into the role of the histidines in the structure and stability of cytochrome c.
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J Biol Inorg Chem,
11,
52-62.
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F.Sinibaldi,
M.C.Piro,
M.Coletta,
and
R.Santucci
(2006).
Salt-induced formation of the A-state of ferricytochrome c--effect of the anion charge on protein structure.
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FEBS J,
273,
5347-5357.
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H.A.Heering,
K.A.Williams,
S.de Vries,
and
C.Dekker
(2006).
Specific vectorial immobilization of oligonucleotide-modified yeast cytochrome C on carbon nanotubes.
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Chemphyschem,
7,
1705-1709.
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K.Murzyn,
T.Róg,
W.Blicharski,
M.Dutka,
J.Pyka,
S.Szytula,
and
W.Froncisz
(2006).
Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.
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Proteins,
62,
1088-1100.
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A.N.Volkov,
D.Ferrari,
J.A.Worrall,
A.M.Bonvin,
and
M.Ubbink
(2005).
The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.
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Protein Sci,
14,
799-811.
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M.Levantino,
Q.Huang,
A.Cupane,
M.Laberge,
A.Hagarman,
and
R.Schweitzer-Stenner
(2005).
The importance of vibronic perturbations in ferrocytochrome c spectra: a reevaluation of spectral properties based on low-temperature optical absorption, resonance Raman, and molecular-dynamics simulations.
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J Chem Phys,
123,
054508.
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S.Hirota,
H.Okumura,
S.Kuroiwa,
N.Funasaki,
and
Y.Watanabe
(2005).
Reduction of ferricytochrome c by tyrosyltyrosylphenylalanine.
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J Biol Inorg Chem,
10,
355-363.
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B.Bonanni,
D.Alliata,
A.R.Bizzarri,
and
S.Cannistraro
(2003).
Topological and electron-transfer properties of yeast cytochrome c adsorbed on bare gold electrodes.
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Chemphyschem,
4,
1183-1188.
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T.Lutz,
W.Neupert,
and
J.M.Herrmann
(2003).
Import of small Tim proteins into the mitochondrial intermembrane space.
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EMBO J,
22,
4400-4408.
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C.E.Nordgren,
D.J.Tobias,
M.L.Klein,
and
J.K.Blasie
(2002).
Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces.
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Biophys J,
83,
2906-2917.
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C.Lange,
and
C.Hunte
(2002).
Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.
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Proc Natl Acad Sci U S A,
99,
2800-2805.
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PDB code:
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D.M.Tiede,
R.Zhang,
and
S.Seifert
(2002).
Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C.
|
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Biochemistry,
41,
6605-6614.
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E.Stellwagen,
E.Olivieri,
and
P.G.Righetti
(2002).
Salt-promoted protein folding, preferential binding, or electrostatic screening?
|
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Proteins,
49,
147-153.
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M.Paoli,
J.Marles-Wright,
and
A.Smith
(2002).
Structure-function relationships in heme-proteins.
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DNA Cell Biol,
21,
271-280.
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O.V.Tsodikov,
M.T.Record,
and
Y.V.Sergeev
(2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
|
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J Comput Chem,
23,
600-609.
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S.Geremia,
G.Garau,
L.Vaccari,
R.Sgarra,
M.S.Viezzoli,
M.Calligaris,
and
L.Randaccio
(2002).
Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.
|
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Protein Sci,
11,
6.
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PDB codes:
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Z.W.Chen,
K.Matsushita,
T.Yamashita,
T.A.Fujii,
H.Toyama,
O.Adachi,
H.D.Bellamy,
and
F.S.Mathews
(2002).
Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
|
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Structure,
10,
837-849.
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PDB code:
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A.Camara-Artigas,
J.C.Williams,
and
J.P.Allen
(2001).
Structure of cytochrome c2 from Rhodospirillum centenum.
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Acta Crystallogr D Biol Crystallogr,
57,
1498-1505.
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PDB code:
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C.Blouin,
J.G.Guillemette,
and
C.J.Wallace
(2001).
Resolving the individual components of a pH-induced conformational change.
|
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Biophys J,
81,
2331-2338.
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J.C.Parrish,
J.G.Guillemette,
and
C.J.Wallace
(2001).
Contribution of leucine 85 to the structure and function of Saccharomyces cerevisiae iso-1 cytochrome c.
|
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Biochem Cell Biol,
79,
517-524.
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M.R.Sawaya,
D.W.Krogmann,
A.Serag,
K.K.Ho,
T.O.Yeates,
and
C.A.Kerfeld
(2001).
Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima.
|
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Biochemistry,
40,
9215-9225.
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PDB codes:
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M.Santana,
M.M.Pereira,
N.P.Elias,
C.M.Soares,
and
M.Teixeira
(2001).
Gene cluster of Rhodothermus marinus high-potential iron-sulfur Protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.
|
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J Bacteriol,
183,
687-699.
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P.D.Barker,
I.Bertini,
R.Del Conte,
S.J.Ferguson,
P.Hajieva,
E.Tomlinson,
P.Turano,
and
M.S.Viezzoli
(2001).
A further clue to understanding the mobility of mitochondrial yeast cytochrome c: a (15)N T1rho investigation of the oxidized and reduced species.
|
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Eur J Biochem,
268,
4468-4476.
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X.J.Morelli,
P.N.Palma,
F.Guerlesquin,
and
A.C.Rigby
(2001).
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
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Protein Sci,
10,
2131-2137.
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A.M.Edwards,
K.Zhang,
C.E.Nordgren,
and
J.K.Blasie
(2000).
Heme structure and orientation in single monolayers of cytochrome c on polar and nonpolar soft surfaces.
|
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Biophys J,
79,
3105-3117.
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D.Zhao,
H.M.Hutton,
P.R.Gooley,
N.E.MacKenzie,
and
M.A.Cusanovich
(2000).
Redox-related conformational changes in Rhodobacter capsulatus cytochrome c2.
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Protein Sci,
9,
1828-1837.
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D.Zhao,
H.M.Hutton,
T.E.Meyer,
F.A.Walker,
N.E.MacKenzie,
and
M.A.Cusanovich
(2000).
Structure and stability effects of the mutation of glycine 34 to serine in Rhodobacter capsulatus cytochrome c(2).
|
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Biochemistry,
39,
4053-4061.
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E.J.Tomlinson,
and
S.J.Ferguson
(2000).
Conversion of a c type cytochrome to a b type that spontaneously forms in vitro from apo protein and heme: implications for c type cytochrome biogenesis and folding.
|
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Proc Natl Acad Sci U S A,
97,
5156-5160.
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F.I.Rosell,
T.R.Harris,
D.P.Hildebrand,
S.Döpner,
P.Hildebrandt,
and
A.G.Mauk
(2000).
Characterization of an alkaline transition intermediate stabilized in the Phe82Trp variant of yeast iso-1-cytochrome c.
|
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Biochemistry,
39,
9047-9054.
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R.M.Kluck,
L.M.Ellerby,
H.M.Ellerby,
S.Naiem,
M.P.Yaffe,
E.Margoliash,
D.Bredesen,
A.G.Mauk,
F.Sherman,
and
D.D.Newmeyer
(2000).
Determinants of cytochrome c pro-apoptotic activity. The role of lysine 72 trimethylation.
|
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J Biol Chem,
275,
16127-16133.
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C.M.Lett,
M.D.Rosu-Myles,
H.E.Frey,
and
J.G.Guillemette
(1999).
Rational design of a more stable yeast iso-1-cytochrome c.
|
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Biochim Biophys Acta,
1432,
40-48.
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I.Bertini,
and
C.Luchinat
(1999).
New applications of paramagnetic NMR in chemical biology.
|
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Curr Opin Chem Biol,
3,
145-151.
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J.A.Kornblatt,
M.J.Kornblatt,
R.Lange,
E.Mombelli,
and
J.G.Guillemette
(1999).
The individual tyrosines of proteins: their spectra may or may not differ from those in water or other solvents.
|
| |
Biochim Biophys Acta,
1431,
238-248.
|
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J.R.Liggins,
T.P.Lo,
G.D.Brayer,
and
B.T.Nall
(1999).
Thermal stability of hydrophobic heme pocket variants of oxidized cytochrome c.
|
| |
Protein Sci,
8,
2645-2654.
|
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J.Read,
R.Gill,
S.L.Dales,
J.B.Cooper,
S.P.Wood,
and
C.Anthony
(1999).
The molecular structure of an unusual cytochrome c2 determined at 2.0 A; the cytochrome cH from Methylobacterium extorquens.
|
| |
Protein Sci,
8,
1232-1240.
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PDB code:
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J.S.Fetrow,
and
S.M.Baxter
(1999).
Assignment of 15N chemical shifts and 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c.
|
| |
Biochemistry,
38,
4480-4492.
|
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M.Laberge,
M.Köhler,
J.M.Vanderkooi,
and
J.Friedrich
(1999).
Sampling field heterogeneity at the heme of c-type cytochromes by spectral hole burning spectroscopy and electrostatic calculations.
|
| |
Biophys J,
77,
3293-3304.
|
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S.M.Baxter,
and
J.S.Fetrow
(1999).
Hydrogen exchange behavior of [U-15N]-labeled oxidized and reduced iso-1-cytochrome c.
|
| |
Biochemistry,
38,
4493-4503.
|
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X.Wang,
and
G.J.Pielak
(1999).
Equilibrium thermodynamics of a physiologically-relevant heme-protein complex.
|
| |
Biochemistry,
38,
16876-16881.
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A.K.Bhuyan,
and
J.B.Udgaonkar
(1998).
Multiple kinetic intermediates accumulate during the unfolding of horse cytochrome c in the oxidized state.
|
| |
Biochemistry,
37,
9147-9155.
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B.Hammack,
K.Attfield,
D.Clayton,
E.Dec,
A.Dong,
C.Sarisky,
and
B.E.Bowler
(1998).
The magnitude of changes in guanidine-HCl unfolding m-values in the protein, iso-1-cytochrome c, depends upon the substructure containing the mutation.
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| |
Protein Sci,
7,
1789-1795.
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J.S.Fetrow,
J.S.Spitzer,
B.M.Gilden,
S.J.Mellender,
T.J.Begley,
B.J.Haas,
and
T.L.Boose
(1998).
Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c.
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| |
Biochemistry,
37,
2477-2487.
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J.S.Fetrow,
U.Dreher,
D.J.Wiland,
D.L.Schaak,
and
T.L.Boose
(1998).
Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c.
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| |
Protein Sci,
7,
994.
|
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L.Banci,
I.Bertini,
M.A.De la Rosa,
D.Koulougliotis,
J.A.Navarro,
and
O.Walter
(1998).
Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.
|
| |
Biochemistry,
37,
4831-4843.
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PDB codes:
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M.Laberge,
K.A.Sharp,
and
J.M.Vanderkooi
(1998).
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Biochemistry,
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PDB code:
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Biochemistry,
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Biochemistry,
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PDB codes:
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Structure,
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PDB code:
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PDB codes:
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PDB codes:
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T.B.Karpishin,
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Cytochrome c6 from Monoraphidium braunii. A cytochrome with an unusual heme axial coordination.
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Eur J Biochem,
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Protein Sci,
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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