Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35657.00 
• Atom Count: 2606 
• Residue Count: 311 
• Unique protein chains: 1

3LO8

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

• DOI: 10.2210/pdb3LO8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Escherichia coli


• Deposited: 2010-02-03 Released: 2010-03-16 
• Deposition Author(s): Faber, H.R., Karplus, P.A.

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Experimental Data Snapshot

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

Literature

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

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

(2010) Acta Crystallogr.,Sect.D 66: 834-842

• PubMed: 20606264 
• DOI: 10.1107/S0907444910019207


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ferredoxin--NADP reductase	A	311	Zea mays	Mutation(s): 0
Find proteins for Q41736 (Zea mays) Go to UniProtKB:  Q41736

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.155 
• R-Value Work: 0.125 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 59.140	α = 90.00
b = 59.140	β = 90.00
c = 186.740	γ = 120.00

Software Package:

Software Name	Purpose
TNT	refinement
DENZO	data reduction
TNT	phasing
SCALEPACK	data scaling
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-03 
• Released Date: 2010-03-16 
• Deposition Author(s): Faber, H.R., Karplus, P.A.

Revision History 

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