3dni

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(New page: 200px<br /><applet load="3dni" size="450" color="white" frame="true" align="right" spinBox="true" caption="3dni, resolution 2.0&Aring;" /> '''CRYSTALLOGRAPHIC REFI...)
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'''CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION'''<br />
'''CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION'''<br />
==Overview==
==Overview==
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The structure of bovine pancreatic deoxyribonuclease I (DNase I) has been, refined at 2 A resolution using the restrained parameter, reciprocal, least-squares procedure of Hendrickson and Konnert. The conventional, R-factor for 16,104 reflections with I greater than or equal to 3 sigma, (I) from 6.0 to 2.0 A resolution is 0.157. Bond lengths and angles of the, refined structure are close to ideal values with root-mean-square (r.m.s.), deviations of 0.023 A and 1.4 degrees, respectively. The r.m.s. deviation, of short non-bonded contacts from the sum of van der Waals' radii is 0.18, A. The orientation of side-chains shows a clear trimodal distribution of, chi 1-angles at -60 degrees, 180 degrees, 60 degrees (in the order of, preference) corresponding to staggered conformations. The chemically, determined sequence was corrected at four positions, the major correction, being an insertion of the tripeptide Ile-Val-Arg between Arg27 and Arg28., Extended hydrophobic regions in between, and on either side of, the two, central six-stranded beta-pleated sheets are mainly responsible for the, low average isotropic temperature factor of 11.9 A2 for the 2033 protein, atoms. Besides the flexible loop region between Gly97 and Gly102 (Glu99, and Ser100 are disordered) and the carbohydrate side-chain, which both, extend into a large solvent channel, only the exposed loop Arg70 to Lys74, shows elevated thermal mobility. The longest of the eight helices in DNase, I, together representing 26% of the structure, has a 22 degree kink and, consists of two alpha-helical segments (residues 136 to 144 and 145 to, 155) separated by a 3(10)-helical turn. DNase I fragments 1 to 120 and 121, to 257 can be superimposed by an approximate 2-fold axis (r.m.s. deviation, 1.49 A for 61 equivalent C alpha positions), suggesting that the enzyme, might be the result of gene duplication. The two Ca2+ bound to DNase I, under crystallization conditions are important for its structural, integrity by stabilizing the surface loop Asp198 to Thr204 and limiting, the region of high thermal mobility in the flexible loop to residues Gly97, to Gly102. The N-linked carbohydrate side-chain attached to Asn18 is of, the high-mannose type with a branching point at the mannose residue in, position 3.(ABSTRACT TRUNCATED AT 400 WORDS)
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The structure of bovine pancreatic deoxyribonuclease I (DNase I) has been refined at 2 A resolution using the restrained parameter, reciprocal least-squares procedure of Hendrickson and Konnert. The conventional R-factor for 16,104 reflections with I greater than or equal to 3 sigma (I) from 6.0 to 2.0 A resolution is 0.157. Bond lengths and angles of the refined structure are close to ideal values with root-mean-square (r.m.s.) deviations of 0.023 A and 1.4 degrees, respectively. The r.m.s. deviation of short non-bonded contacts from the sum of van der Waals' radii is 0.18 A. The orientation of side-chains shows a clear trimodal distribution of chi 1-angles at -60 degrees, 180 degrees, 60 degrees (in the order of preference) corresponding to staggered conformations. The chemically determined sequence was corrected at four positions, the major correction being an insertion of the tripeptide Ile-Val-Arg between Arg27 and Arg28. Extended hydrophobic regions in between, and on either side of, the two central six-stranded beta-pleated sheets are mainly responsible for the low average isotropic temperature factor of 11.9 A2 for the 2033 protein atoms. Besides the flexible loop region between Gly97 and Gly102 (Glu99 and Ser100 are disordered) and the carbohydrate side-chain, which both extend into a large solvent channel, only the exposed loop Arg70 to Lys74 shows elevated thermal mobility. The longest of the eight helices in DNase I, together representing 26% of the structure, has a 22 degree kink and consists of two alpha-helical segments (residues 136 to 144 and 145 to 155) separated by a 3(10)-helical turn. DNase I fragments 1 to 120 and 121 to 257 can be superimposed by an approximate 2-fold axis (r.m.s. deviation 1.49 A for 61 equivalent C alpha positions), suggesting that the enzyme might be the result of gene duplication. The two Ca2+ bound to DNase I under crystallization conditions are important for its structural integrity by stabilizing the surface loop Asp198 to Thr204 and limiting the region of high thermal mobility in the flexible loop to residues Gly97 to Gly102. The N-linked carbohydrate side-chain attached to Asn18 is of the high-mannose type with a branching point at the mannose residue in position 3.(ABSTRACT TRUNCATED AT 400 WORDS)
==About this Structure==
==About this Structure==
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3DNI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3DNI OCA].
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3DNI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNI OCA].
==Reference==
==Reference==
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[[Category: endonuclease]]
[[Category: endonuclease]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:39:16 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:09:13 2008''

Revision as of 17:09, 21 February 2008

Image:3dni.jpg

3dni, resolution 2.0Å

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CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION

Overview

The structure of bovine pancreatic deoxyribonuclease I (DNase I) has been refined at 2 A resolution using the restrained parameter, reciprocal least-squares procedure of Hendrickson and Konnert. The conventional R-factor for 16,104 reflections with I greater than or equal to 3 sigma (I) from 6.0 to 2.0 A resolution is 0.157. Bond lengths and angles of the refined structure are close to ideal values with root-mean-square (r.m.s.) deviations of 0.023 A and 1.4 degrees, respectively. The r.m.s. deviation of short non-bonded contacts from the sum of van der Waals' radii is 0.18 A. The orientation of side-chains shows a clear trimodal distribution of chi 1-angles at -60 degrees, 180 degrees, 60 degrees (in the order of preference) corresponding to staggered conformations. The chemically determined sequence was corrected at four positions, the major correction being an insertion of the tripeptide Ile-Val-Arg between Arg27 and Arg28. Extended hydrophobic regions in between, and on either side of, the two central six-stranded beta-pleated sheets are mainly responsible for the low average isotropic temperature factor of 11.9 A2 for the 2033 protein atoms. Besides the flexible loop region between Gly97 and Gly102 (Glu99 and Ser100 are disordered) and the carbohydrate side-chain, which both extend into a large solvent channel, only the exposed loop Arg70 to Lys74 shows elevated thermal mobility. The longest of the eight helices in DNase I, together representing 26% of the structure, has a 22 degree kink and consists of two alpha-helical segments (residues 136 to 144 and 145 to 155) separated by a 3(10)-helical turn. DNase I fragments 1 to 120 and 121 to 257 can be superimposed by an approximate 2-fold axis (r.m.s. deviation 1.49 A for 61 equivalent C alpha positions), suggesting that the enzyme might be the result of gene duplication. The two Ca2+ bound to DNase I under crystallization conditions are important for its structural integrity by stabilizing the surface loop Asp198 to Thr204 and limiting the region of high thermal mobility in the flexible loop to residues Gly97 to Gly102. The N-linked carbohydrate side-chain attached to Asn18 is of the high-mannose type with a branching point at the mannose residue in position 3.(ABSTRACT TRUNCATED AT 400 WORDS)

About this Structure

3DNI is a Single protein structure of sequence from [1] with as ligand. Active as Deoxyribonuclease I, with EC number 3.1.21.1 Full crystallographic information is available from OCA.

Reference

Crystallographic refinement and structure of DNase I at 2 A resolution., Oefner C, Suck D, J Mol Biol. 1986 Dec 5;192(3):605-32. PMID:3560229

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