1plc
From Proteopedia
(New page: 200px<br /><applet load="1plc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1plc, resolution 1.33Å" /> '''ACCURACY AND PRECISI...) |
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| - | [[Image:1plc.gif|left|200px]]<br /><applet load="1plc" size=" | + | [[Image:1plc.gif|left|200px]]<br /><applet load="1plc" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1plc, resolution 1.33Å" /> | caption="1plc, resolution 1.33Å" /> | ||
'''ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION'''<br /> | '''ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the electron-transfer protein, plastocyanin (99 amino | + | The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = 46.86 (3), c = 57.60 (3) A. The 14,303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 A and the root-mean-square difference between the positions of the C alpha atoms in this refined model and in the structure previously refined at 1.6 A resolution is 0.11 A. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A. |
==About this Structure== | ==About this Structure== | ||
| - | 1PLC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra] with CU as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | + | 1PLC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Populus_nigra Populus nigra] with <scene name='pdbligand=CU:'>CU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1PCY. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLC OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Populus nigra]] | [[Category: Populus nigra]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Freeman, H | + | [[Category: Freeman, H C.]] |
| - | [[Category: Guss, J | + | [[Category: Guss, J M.]] |
[[Category: CU]] | [[Category: CU]] | ||
[[Category: electron transport]] | [[Category: electron transport]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:30:03 2008'' |
Revision as of 12:30, 21 February 2008
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ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION
Overview
The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = 46.86 (3), c = 57.60 (3) A. The 14,303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 A and the root-mean-square difference between the positions of the C alpha atoms in this refined model and in the structure previously refined at 1.6 A resolution is 0.11 A. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A.
About this Structure
1PLC is a Single protein structure of sequence from Populus nigra with as ligand. This structure supersedes the now removed PDB entry 1PCY. Full crystallographic information is available from OCA.
Reference
Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution., Guss JM, Bartunik HD, Freeman HC, Acta Crystallogr B. 1992 Dec 1;48 ( Pt 6):790-811. PMID:1492962
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