7rxn: Difference between revisions

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[[Image:7rxn.gif|left|200px]]<br /><applet load="7rxn" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:7rxn.gif|left|200px]]<br /><applet load="7rxn" size="350" color="white" frame="true" align="right" spinBox="true"

caption="7rxn, resolution 1.5Å" />

'''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''<br />

==Overview==

The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined, against 1.5 A X-ray diffraction data collected on a diffractometer. The, final model comprises 395 non-hydrogen protein atoms, and 180 solvent O, atoms. The final R-value for the model with calculated H atom positions, included as fixed contributions is 0.098 over all reflections greater than, 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated, to be 0.08 A. The solvent model was twice redetermined during the later, stages of refinement and was instrumental in its success. One sequence, error has been detected and corrected (Thr21----Asp). The iron-sulfur site, bond angles are distorted from true tetrahedral symmetry, as found in, other rubredoxin structures. A significant deviation from tetrahedral, angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the, loops binding the iron atom. The planes of two aromatic groups, Tyr4 and, Trp37, are nearly parallel to, and lie under, an extended system of atoms, that includes the peptide bonds preceding the first cysteine residue of, each cysteine loop as well as the cysteine side-chain, the iron, and the, cysteine side-chain of the opposite loop, forming a previously, unrecognized extended system that may function in electron transfer.

The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X-ray diffraction data collected on a diffractometer. The final model comprises 395 non-hydrogen protein atoms, and 180 solvent O atoms. The final R-value for the model with calculated H atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp). The iron-sulfur site bond angles are distorted from true tetrahedral symmetry, as found in other rubredoxin structures. A significant deviation from tetrahedral angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the loops binding the iron atom. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-chain, the iron, and the cysteine side-chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.

==About this Structure==

7RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. This structure ~~superseeds~~ the now removed PDB entry 3RXN. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].

7RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 3RXN. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].

==Reference==

Line 13:

[[Category: Desulfovibrio vulgaris]]

[[Category: Single protein]]

[[Category: Adman, E.T.]]

[[Category: Adman, E T.]]

[[Category: Jensen, L.H.]]

[[Category: Jensen, L H.]]

[[Category: Sieker, L.C.]]

[[Category: Sieker, L C.]]

[[Category: FE]]

[[Category: SO4]]

[[Category: electron transfer(iron-sulfur protein)]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Tue Nov 20 15~~:11:~~21 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:17:33 2008''

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@@ Line 1: / Line 1: @@
-[[Image:7rxn.gif|left|200px]]<br /><applet load="7rxn" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:7rxn.gif|left|200px]]<br /><applet load="7rxn" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="7rxn, resolution 1.5&Aring;" />
 '''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''<br />
 ==Overview==
-The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined, against 1.5 A X-ray diffraction data collected on a diffractometer. The, final model comprises 395 non-hydrogen protein atoms, and 180 solvent O, atoms. The final R-value for the model with calculated H atom positions, included as fixed contributions is 0.098 over all reflections greater than, 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated, to be 0.08 A. The solvent model was twice redetermined during the later, stages of refinement and was instrumental in its success. One sequence, error has been detected and corrected (Thr21----Asp). The iron-sulfur site, bond angles are distorted from true tetrahedral symmetry, as found in, other rubredoxin structures. A significant deviation from tetrahedral, angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the, loops binding the iron atom. The planes of two aromatic groups, Tyr4 and, Trp37, are nearly parallel to, and lie under, an extended system of atoms, that includes the peptide bonds preceding the first cysteine residue of, each cysteine loop as well as the cysteine side-chain, the iron, and the, cysteine side-chain of the opposite loop, forming a previously, unrecognized extended system that may function in electron transfer.
+The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X-ray diffraction data collected on a diffractometer. The final model comprises 395 non-hydrogen protein atoms, and 180 solvent O atoms. The final R-value for the model with calculated H atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp). The iron-sulfur site bond angles are distorted from true tetrahedral symmetry, as found in other rubredoxin structures. A significant deviation from tetrahedral angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the loops binding the iron atom. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-chain, the iron, and the cysteine side-chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.
 ==About this Structure==
-RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FE and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 3RXN. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].
+RXN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 3RXN. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Desulfovibrio vulgaris]]
 [[Category: Single protein]]
-[[Category: Adman, E.T.]]
+[[Category: Adman, E T.]]
-[[Category: Jensen, L.H.]]
+[[Category: Jensen, L H.]]
-[[Category: Sieker, L.C.]]
+[[Category: Sieker, L C.]]
 [[Category: FE]]
 [[Category: SO4]]
 [[Category: electron transfer(iron-sulfur protein)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:11:21 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:17:33 2008''