3LO8

Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms

Summary for 3LO8

• Entry DOI: 10.2210/pdb3lo8/pdb
• Related: 1JB9
• Descriptor: Ferredoxin--NADP reductase, FLAVIN-ADENINE DINUCLEOTIDE, SODIUM ION, ... (4 entities in total)
• Functional Keywords: electron transport, oxidoreductase, fad, flavoprotein, nadp
• Biological source: Zea mays (maize)
• Total number of polymer chains: 1
• Total formula weight: 35657.00

Authors

Faber, H.R.,Karplus, P.A. (deposition date: 2010-02-03, release date: 2010-03-16, Last modification date: 2024-10-16)

Primary citation

Tronrud, D.E.,Berkholz, D.S.,Karplus, P.A.
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
Acta Crystallogr.,Sect.D, 66:834-842, 2010

PubMed Abstract: The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the phi/psi angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm.

PubMed: 20606264
DOI: 10.1107/S0907444910019207

Experimental method

X-RAY DIFFRACTION (1.05 Å)