1J8Q

Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris Wild-type at 1.35 Angstrom Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

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Literature

Comparison of the refined crystal structures of wild-type (1.34 A) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 A) at 100 K.

Artali, R., Bombieri, G., Meneghetti, F., Gilardi, G., Sadeghi, S.J., Cavazzini, D., Rossi, G.L.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1787-1792

  • DOI: 10.1107/s0907444902012234
  • Primary Citation of Related Structures:  
    1J8Q, 1J9E, 1J9G

  • PubMed Abstract: 

    • Engineered flavodoxins in which a surface residue has been replaced by an exposed cysteine are useful modules to link multi-domain redox proteins obtained by gene fusion to electrode surfaces. In the present work, the crystal structure of the S35C mutant of Desulfovibrio vulgaris flavodoxin in the oxidized state has been determined and compared with a refined structure of the wild type (wt) ...

    Engineered flavodoxins in which a surface residue has been replaced by an exposed cysteine are useful modules to link multi-domain redox proteins obtained by gene fusion to electrode surfaces. In the present work, the crystal structure of the S35C mutant of Desulfovibrio vulgaris flavodoxin in the oxidized state has been determined and compared with a refined structure of the wild type (wt). The structure of wt flavodoxin (space group P4(3)2(1)2, unit-cell parameters a = 50.52, b = 50.52, c = 138.59 A) at 1.34 A resolution has been refined to R = 0.16 and R(free) = 0.18. The structure of the S35C mutant (space group P4(3)2(1)2, unit-cell parameters a = 50.55, b = 50.55, c = 138.39 A) at 1.44 A resolution has been refined to R = 0.13 and R(free) = 0.16. Data sets were collected with synchrotron radiation at 100 K. In the S35C mutant, the Cys35 thiol group points towards a hydrophobic region, whilst in the wt the Ser35 hydroxyl group points towards a more polar region. The solvent exposure of Cys35 is 43 A(2), of which 8 A(2) is for the sulfur. This is comparable to the exposure of 48 A(2) found for the wt Ser35, where that of the hydroxyl oxygen is also 8 A(2).

    Organizational Affiliation: 

    Institute of Pharmaceutical Chemistry, University of Milano, Italy.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVODOXINA147Desulfovibrio vulgarisMutation(s): 0 
UniProt
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00323
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 Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.52α = 90
b = 50.52β = 90
c = 138.59γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97model building
SHELXL-97refinement
CCP4data scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance