2D5M | pdb_00002d5m

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

• PDB DOI: https://doi.org/10.2210/pdb2D5M/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-11-02 Released: 2006-11-21 
• Deposition Author(s): Ueda, Y., Shibata, N., Higuchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)

Ueda, Y., Shibata, N., Higuchi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 21.69 kDa 
• Atom Count: 1,744 
• Modeled Residue Count: 183 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
flavoredoxin	A	190	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0
UniProt
Find proteins for Q4W5X6 (Nitratidesulfovibrio vulgaris) Explore Q4W5X6  Go to UniProtKB:  Q4W5X6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.346	α = 90
b = 53.346	β = 90
c = 116.224	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Ueda, Y., Shibata, N., Higuchi, Y.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations