3pmg
From Proteopedia
(New page: 200px<br /><applet load="3pmg" size="450" color="white" frame="true" align="right" spinBox="true" caption="3pmg, resolution 2.4Å" /> '''STRUCTURE OF RABBIT M...) |
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| - | [[Image:3pmg.jpg|left|200px]]<br /><applet load="3pmg" size=" | + | [[Image:3pmg.jpg|left|200px]]<br /><applet load="3pmg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3pmg, resolution 2.4Å" /> | caption="3pmg, resolution 2.4Å" /> | ||
'''STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY'''<br /> | '''STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to | + | Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (Rfree = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 A and 3.2 degrees, respectively. Features of the protein that were recognized only in the revised model include: the disposition of water molecules within domain-domain interfaces; two ion pairs buried in domain-domain interfaces, one of which is a structural arginine around which the active-site phosphoserine loop is wound; the basic architecture of the active-site 'crevice', which is a groove in a 1(1/3)-turn helix, open at both ends, that is produced by the interfacing of the four domains; the distorted hexacoordinate ligand sphere of the active-site Mg2+, where the enzymic phosphate group acts as a bidentate ligand; a pair of arginine residues in domain IV that form part of the enzymic phosphate-binding site (distal subsite) whose disposition in the two monomers of the asymmetric unit is affected unequally by distant crystallographic contacts; structural differences throughout domain IV, produced by these differing contacts, that may mimic solution differences induced by substrate binding; large differences in individually refined Debye-Waller thermal factors for corresponding main-chain atoms in monomers (1) and (2), suggesting a dynamic disorder within the crystal that may involve domain-size groups of residues; and a 'nucleophilic elbow' in the active site that resides in a topological environment differing from previous descriptions of this type of structure in other proteins. |
==About this Structure== | ==About this Structure== | ||
| - | 3PMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | + | 3PMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 2PMG. Active as [http://en.wikipedia.org/wiki/Phosphoglucomutase Phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.2 5.4.2.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PMG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Baranidharan, S.]] | [[Category: Baranidharan, S.]] | ||
| - | [[Category: Junior, W | + | [[Category: Junior, W J.Ray.]] |
[[Category: Liu, Y.]] | [[Category: Liu, Y.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
[[Category: phosphoglucomutase]] | [[Category: phosphoglucomutase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:10:56 2008'' |
Revision as of 17:10, 21 February 2008
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STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY
Overview
Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (Rfree = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 A and 3.2 degrees, respectively. Features of the protein that were recognized only in the revised model include: the disposition of water molecules within domain-domain interfaces; two ion pairs buried in domain-domain interfaces, one of which is a structural arginine around which the active-site phosphoserine loop is wound; the basic architecture of the active-site 'crevice', which is a groove in a 1(1/3)-turn helix, open at both ends, that is produced by the interfacing of the four domains; the distorted hexacoordinate ligand sphere of the active-site Mg2+, where the enzymic phosphate group acts as a bidentate ligand; a pair of arginine residues in domain IV that form part of the enzymic phosphate-binding site (distal subsite) whose disposition in the two monomers of the asymmetric unit is affected unequally by distant crystallographic contacts; structural differences throughout domain IV, produced by these differing contacts, that may mimic solution differences induced by substrate binding; large differences in individually refined Debye-Waller thermal factors for corresponding main-chain atoms in monomers (1) and (2), suggesting a dynamic disorder within the crystal that may involve domain-size groups of residues; and a 'nucleophilic elbow' in the active site that resides in a topological environment differing from previous descriptions of this type of structure in other proteins.
About this Structure
3PMG is a Single protein structure of sequence from Oryctolagus cuniculus with as ligand. This structure supersedes the now removed PDB entry 2PMG. Active as Phosphoglucomutase, with EC number 5.4.2.2 Full crystallographic information is available from OCA.
Reference
Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution., Liu Y, Ray WJ Jr, Baranidharan S, Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):392-405. PMID:15299905
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