2ARK | pdb_00002ark

Structure of a flavodoxin from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2ARK/pdb

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


• Deposited: 2005-08-19 Released: 2005-10-25 
• Deposition Author(s): Cuff, M.E., Quartey, P., Zhou, M., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Structure of a flavodoxin from Aquifex aeolicus

Cuff, M.E., Quartey, P., Zhou, M., Cymborowski, M., Minor, W., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 127.56 kDa 
• Atom Count: 9,119 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin	A, B, C, D, E, F	188	Aquifex aeolicus	Mutation(s): 7  Gene Names: fldA, floX
UniProt
Find proteins for O67866 (Aquifex aeolicus (strain VF5)) Explore O67866  Go to UniProtKB:  O67866

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], J [auth B], L [auth C], O [auth D], Q [auth E], R [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], P [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.846	α = 90
b = 112.846	β = 90
c = 150.648	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
RESOLVE	phasing
DM	phasing
Coot	model building
O	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Cuff, M.E., Quartey, P., Zhou, M., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary