3LO8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.

Tronrud, D.E.Berkholz, D.S.Karplus, P.A.

(2010) Acta Crystallogr D Biol Crystallogr 66: 834-842

  • DOI: 10.1107/S0907444910019207
  • Primary Citation of Related Structures:  
    3LO8

  • 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 ...

    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.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Oregon State University, Corvallis, Oregon 97331, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferredoxin--NADP reductaseA311Zea maysMutation(s): 0 
EC: 1.18.1.2
Find proteins for Q41736 (Zea mays)
Explore Q41736 
Go to UniProtKB:  Q41736
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.125 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.14α = 90
b = 59.14β = 90
c = 186.74γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description