3O3K

Crystal structure of AF1382 from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.

Zhu, J.Y.Fu, Z.Q.Chen, L.Xu, H.Chrzas, J.Rose, J.Wang, B.C.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1242-1252

  • DOI: https://doi.org/10.1107/S0907444912026212
  • Primary Citation of Related Structures:  
    3O3K, 3OV8

  • PubMed Abstract: 

    The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF(anom)/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R(free) = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R(free) = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein AF_138295Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF_1382
UniProt
Find proteins for O28889 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28889 
Go to UniProtKB:  O28889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28889
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.54α = 90
b = 53.54β = 90
c = 41.25γ = 90
Software Package:
Software NamePurpose
SGXPROmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-04
    Changes: Database references
  • Version 1.3: 2012-09-19
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references