3LO8 | pdb_00003lo8

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

• PDB DOI: https://doi.org/10.2210/pdb3LO8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• 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 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.125 (Depositor) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

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

• PubMed: 20606264 
• DOI: https://doi.org/10.1107/S0907444910019207
• Primary Citation 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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 35.66 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 302 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin--NADP reductase	A	311	Zea mays	Mutation(s): 0  EC: 1.18.1.2
UniProt
Find proteins for Q41736 (Zea mays) Explore Q41736  Go to UniProtKB:  Q41736

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.155 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.125 (Depositor) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.14	α = 90
b = 59.14	β = 90
c = 186.74	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary