1VM9 | pdb_00001vm9

The X-ray Structure of the cys84ala cys85ala double mutant of the [2Fe-2S] Ferredoxin subunit of Toluene-4-Monooxygenase from Pseudomonas Mendocina KR1

• PDB DOI: https://doi.org/10.2210/pdb1VM9/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Ectopseudomonas mendocina
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-09-13 Released: 2004-09-21 
• Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bingman, C.A., Allard, S.T.M., Moe, L.A., Fox, B.G., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q3W

Literature

Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.

Moe, L.A., Bingman, C.A., Wesenberg, G.E., Phillips, G.N., Fox, B.G.

(2006) Acta Crystallogr D Biol Crystallogr 62: 476-482

• PubMed: 16627939 
• DOI: https://doi.org/10.1107/S0907444906006056
• Primary Citation Related Structures: 
  1VM9


• PubMed Abstract: 
  

  The structure of the Rieske-type ferredoxin (T4moC) from toluene 4-monooxygenase was determined by X-ray crystallography in the [2Fe-2S](2+) state at a resolution of 1.48 A using single-wavelength anomalous dispersion phasing with the [2Fe-2S] center. The structure consists of ten beta-strands arranged into the three antiparallel beta-sheet topology observed in all Rieske proteins. Trp69 of T4moC is adjacent to the [2Fe-2S] centre, which displaces a loop containing the conserved Pro81 by approximately 8 A away from the [2Fe-2S] cluster compared with the Pro loop in the closest structural and functional homolog, the Rieske-type ferredoxin BphF from biphenyl dioxygenase. In addition, T4moC contains five hydrogen bonds to the [2Fe-2S] cluster compared with three hydrogen bonds in BphF. Moreover, the electrostatic surface of T4moC is distinct from that of BphF. These structural differences are identified as possible contributors to the evolutionary specialization of soluble Rieske-type ferredoxins between the diiron monooxygenases and cis-dihydrodiol-forming dioxygenases.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin-Madison, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.55 kDa 
• Atom Count: 996 
• Modeled Residue Count: 109 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toluene-4-monooxygenase system protein C	A	111	Ectopseudomonas mendocina	Mutation(s): 2  Gene Names: tmoC
UniProt
Find proteins for Q00458 (Ectopseudomonas mendocina) Explore Q00458  Go to UniProtKB:  Q00458

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	D [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.51	α = 90
b = 52.4	β = 90
c = 83.556	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bingman, C.A., Allard, S.T.M., Moe, L.A., Fox, B.G., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection