3VYA | pdb_00003vya

W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

• PDB DOI: https://doi.org/10.2210/pdb3VYA/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-22 Released: 2013-09-25 
• Deposition Author(s): Takagi, R., Nakanishi, T., Kitamura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Takagi, R., Nakanishi, T., Kitamura, M.

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 (software)

Macromolecule Content 

• Total Structure Weight: 13.59 kDa 
• Atom Count: 972 
• Modeled Residue Count: 120 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A	122	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 1  Gene Names: DvMF_2023
UniProt
Find proteins for Q46604 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore Q46604  Go to UniProtKB:  Q46604

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.119	α = 90
b = 44.119	β = 90
c = 178.59	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Takagi, R., Nakanishi, T., Kitamura, M.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description