1FLM

DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.182 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

How do the x-ray structure and the NMR structure of FMN-binding protein differ?

Suto, K.Kawagoe, K.Shibata, N.Morimoto, Y.Higuchi, Y.Kitamura, M.Nakaya, T.Yasuoka, N.

(2000) Acta Crystallogr D Biol Crystallogr 56: 368-371

  • DOI: 10.1107/s0907444900000111
  • Primary Citation of Related Structures:  
    1FLM

  • PubMed Abstract: 
  • The crystal structure of FMN-binding protein (FMN-bp) from Desulfovibrio vulgaris Miyazaki F was solved by the multiple isomorphous replacement method and refined to an R factor of 15.1% at 1.3 A resolution. FMN-bp exists in a dimeric form in the cry ...

    The crystal structure of FMN-binding protein (FMN-bp) from Desulfovibrio vulgaris Miyazaki F was solved by the multiple isomorphous replacement method and refined to an R factor of 15.1% at 1.3 A resolution. FMN-bp exists in a dimeric form in the crystal, in contrast to the monomeric structure determined by NMR. R.m.s. deviations between the crystal structure and the solution structure are more than 2 A, which implies significant differences. There are some hydrophobic residues in the interface between the two monomers. In particular, Leu122 in the C-terminus has a close contact with the o-xylene moiety of FMN, while solvent molecules may cover the o-xylene moiety in the solution structure.


    Organizational Affiliation

    Department of Life Science, Faculty of Science, Himeji Institute of Technology, 3-2-1 Kouto, Kamigori Ako-gun, Hyogo 678-1297, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (FMN-BINDING PROTEIN)AB122Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: DvMF_2023
Find proteins for Q46604 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore Q46604 
Go to UniProtKB:  Q46604
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd :  0.4300000071525574   nM  PDBBind
FMNKd:  0.4300000071525574   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.182 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.23α = 90
b = 84.6β = 94.1
c = 41.11γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-06
    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: 2014-11-26
    Changes: Other