2apr: Difference between revisions

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STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS

OverviewOverview

The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 A, and for angle distances it is 0.034 A. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile "flap", a beta-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.

About this StructureAbout this Structure

2APR is a Single protein structure of sequence from Rhizopus microsporus var. chinensis with as ligand. This structure supersedes the now removed PDB entry 1APR. Active as Hydrolase, with EC number 3.4.23.18, 3.4.23.28 and 3.4.23.30 3.4.21.103, 3.4.23.18, 3.4.23.28 and 3.4.23.30 Full crystallographic information is available from OCA.

ReferenceReference

Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis., Suguna K, Bott RR, Padlan EA, Subramanian E, Sheriff S, Cohen GH, Davies DR, J Mol Biol. 1987 Aug 20;196(4):877-900. PMID:3316666

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-[[Image:2apr.gif|left|200px]]<br /><applet load="2apr" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2apr.gif|left|200px]]<br /><applet load="2apr" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2apr, resolution 1.8&Aring;" />
 '''STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS'''<br />
 ==Overview==
-The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase, from Rhizopus chinensis, has been refined to a crystallographic R-factor, of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have, been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the, final model, the r.m.s. deviation from ideality for bond distances is, 0.010 A, and for angle distances it is 0.034 A. During the course of the, refinement, a calcium ion and 373 water molecules, of which 17 are, internal, have been located. The active aspartate residues, Asp35 and, Asp218, are involved in similar hydrogen-bonding interactions with, neighboring residues and with several water molecules. One water molecule, is located between the two carboxyl groups of the catalytic aspartate, residues in a tightly hydrogen-bonded position. The refinement resulted in, an unambiguous interpretation of the highly mobile "flap", a beta-hairpin, loop region that projects over the binding pocket. Large solvent channels, are formed when the molecules pack in the crystal, exposing the binding, pocket and making it easily accessible. Intermolecular contacts involve, mainly solvent molecules and a few protein atoms. The three-dimensional, structure of rhizopuspepsin closely resembles other aspartic proteinase, structures. A detailed comparison with the structure of penicillopepsin, showed striking similarities as well as subtle differences in the active, site geometry and molecular packing.
+The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 A, and for angle distances it is 0.034 A. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile "flap", a beta-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.
 ==About this Structure==
-APR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhizopus_microsporus_var._chinensis Rhizopus microsporus var. chinensis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1APR. Active as [http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.103, 3.4.23.18, 3.4.23.28 and 3.4.23.30 3.4.21.103, 3.4.23.18, 3.4.23.28 and 3.4.23.30] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2APR OCA].
+APR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhizopus_microsporus_var._chinensis Rhizopus microsporus var. chinensis] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1APR. Active as [http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.103, 3.4.23.18, 3.4.23.28 and 3.4.23.30 3.4.21.103, 3.4.23.18, 3.4.23.28 and 3.4.23.30] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2APR OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Rhizopus microsporus var. chinensis]]
 [[Category: Single protein]]
-[[Category: Davies, D.R.]]
+[[Category: Davies, D R.]]
 [[Category: Suguna, K.]]
 [[Category: CA]]
 [[Category: hydrolase (aspartic proteinase)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:16:39 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:29:38 2008''