Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.12 kDa 
• Atom Count: 449 
• Modelled Residue Count: 53 
• Deposited Residue Count: 54 
• Unique protein chains: 1

1T9Q

Crystal Structure of V44L Cp Rubredoxin

• PDB DOI: 10.2210/pdb1T9Q/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Clostridium pasteurianum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-18 Released: 2004-10-05 
• Deposition Author(s): Park, I.Y., Eidsness, M.K., Lin, I.J., Gebel, E.B., Youn, B., Harley, J.L., Machonkin, T.E., Frederick, R.O., Markley, J.L., Smith, E.T., Ichiye, T., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: Effects of side-chain size on reduction potential.

Park, I.Y., Eidsness, M.K., Lin, I.J., Gebel, E.B., Youn, B., Harley, J.L., Machonkin, T.E., Frederick, R.O., Markley, J.L., Smith, E.T., Ichiye, T., Kang, C.

(2004) Proteins 57: 618-618

• PubMed: 15382226 
• DOI: 10.1002/prot.20243
• Primary Citation of Related Structures:  
  1T9O, 1T9P, 1T9Q


• PubMed Abstract: 
  

Understanding the structural origins of differences in reduction potentials is crucial to understanding how various electron transfer proteins modulate their reduction potentials and how they evolve for diverse functional roles. Here, the high-resolution structures of several Clostridium pasteurianum rubredoxin (Cp Rd) variants with changes in the vicinity of the redox site are reported in order to increase this understanding. Our crystal structures of [V44L] (at 1.8 A resolution), [V44A] (1.6 A), [V44G] (2.0 A) and [V44A, G45P] (1.5 A) Rd (all in their oxidized states) show that there is a gradual decrease in the distance between Fe and the amide nitrogen of residue 44 upon reduction in the size of the side chain of residue 44; the decrease occurs from leucine to valine, alanine or glycine and is accompanied by a gradual increase in their reduction potentials. Mutation of Cp Rd at position 44 also changes the hydrogen-bond distance between the amide nitrogen of residue 44 and the sulfur of cysteine 42 in a size-dependent manner. Our results suggest that residue 44 is an important determinant of Rd reduction potential in a manner dictated by side-chain size. Along with the electric dipole moment of the 43-44 peptide bond and the 44-42 NH--S type hydrogen bond, a modulation mechanism for solvent accessibility through residue 41 might regulate the redox reaction of the Rds.

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Organizational Affiliation: 

School of Molecular Biosciences, Washington State University, Pullman 99164-4660, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	54	Clostridium pasteurianum	Mutation(s): 1
UniProt
Find proteins for P00268 (Clostridium pasteurianum) Explore P00268  Go to UniProtKB:  P00268

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.77	α = 90
b = 63.77	β = 90
c = 32.76	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
CrystalClear	data reduction
AMoRE	phasing
X-PLOR	refinement
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-18 
• Released Date: 2004-10-05 
Deposition Author(s): Park, I.Y., Eidsness, M.K., Lin, I.J., Gebel, E.B., Youn, B., Harley, J.L., Machonkin, T.E., Frederick, R.O., Markley, J.L., Smith, E.T., Ichiye, T., Kang, C.

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations