3F90 | pdb_00003f90

Desulfovibrio desulfuricans (ATCC 29577) semiquinone flavodoxin

• PDB DOI: https://doi.org/10.2210/pdb3F90/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Desulfovibrio desulfuricans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-11-13 Released: 2009-11-17 
• Deposition Author(s): Guelker, M., Shamoo, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Structure of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin in the semiquinone state

Guelker, M., Shamoo, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 129.3 kDa 
• Atom Count: 9,221 
• Modeled Residue Count: 1,176 
• Deposited Residue Count: 1,184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin	A, B, C [auth D], D [auth E], E [auth F], F [auth H], G [auth I], H [auth G]	148	Desulfovibrio desulfuricans	Mutation(s): 1  Gene Names: flavodoxin
UniProt
Find proteins for P26492 (Desulfovibrio desulfuricans) Explore P26492  Go to UniProtKB:  P26492

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	I [auth A], J [auth B], K [auth D], L [auth E], M [auth F], N [auth H], O [auth I], P [auth G]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.893	α = 90
b = 94.893	β = 90
c = 238.09	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Guelker, M., Shamoo, Y.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2019-08-14
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description