1RKR

CRYSTAL STRUCTURE OF AZURIN-I FROM ALCALIGENES XYLOSOXIDANS NCIMB 11015


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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This is version 1.2 of the entry. See complete history


Literature

Structure of azurin I from the denitrifying bacterium Alcaligenes xylosoxidans NCIMB 11015 at 2.45 A resolution.

Li, C.Inoue, T.Gotowda, M.Suzuki, S.Yamaguchi, K.Kunishige, K.Kai, Y.

(1998) Acta Crystallogr D Biol Crystallogr 54: 347-354

  • DOI: 10.1107/s0907444997010974
  • Primary Citation of Related Structures:  
    1RKR

  • PubMed Abstract: 
  • Azurin I from Alcaligenes xylosoxidans NCIMB 11015 (AzN-I) was crystallized by using PEG 4000 as a precipitant. The crystals belong to the monoclinic crystal system and have a space group C2 with the unit-cell parameters of a = 130.67, b = 54.26, c = 74.55 A, and beta = 95 ...

    Azurin I from Alcaligenes xylosoxidans NCIMB 11015 (AzN-I) was crystallized by using PEG 4000 as a precipitant. The crystals belong to the monoclinic crystal system and have a space group C2 with the unit-cell parameters of a = 130.67, b = 54.26, c = 74.55 A, and beta = 95.99 degrees. The structure of AzN-I has been solved by the molecular replacement method. Azurin II from the same bacterium (AzN-II) was chosen as the initial structural model. The final crystallographic R value is 17.3% and free R value is 23.6% for 10958 reflections at a resolution of 2.45 A. The root-mean-square deviations for main-chain atoms range between 0.19 and 0.26 A among the four independent molecules in the asymmetric unit. The Cu atom is coordinated to Ndelta of His46 and His117 at 2.0 (1) and 1.9 (1) A, and to Sgamma of Cys112 at 2.2 (1) A, while the carbonyl O atom of Gly45 and Sdelta of Met121 coordinate axially to Cu atom at 2.5 (1) and 3.1 (1) A, respectively. The Cu-N and Cu-S distances of AzN-I are quite similar to those of AzN-II, however, the Cu-SO (Gly45) bond length in AzN-I is 0.25 A shorter than the counterpart in AzN-II. The results have been used to discuss the differences in the spectra of these two proteins.


    Related Citations: 
    • Isolation and Characterization of Two Distinct Azurins from Alcaligenes Xylosoxidans Subsp. Xylosoxidans Ncib11015 or Gifu1051
      Yamaguchi, K., Deligeer, Nakamura, N., Shidara, S., Iwasaki, H., Suzuki, S.
      (1995) Chem Lett 5: 353
    • Structure of Azurin from Achromobacter Xylosoxidans Ncib11015 at 2.5 A Resolution
      Inoue, T., Shibata, N., Nakanishi, H., Koyama, S., Ishii, H., Kai, Y., Harada, S., Kasai, N., Ohshiro, Y., Suzuki, S., Kohzuma, T., Yamaguchi, K., Shidara, S., Iwasaki, H.
      (1994) J Biochem 116: 1193

    Organizational Affiliation

    Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AZURIN-IA, B, C, D129Achromobacter xylosoxidansMutation(s): 0 
UniProt
Find proteins for P56547 (Alcaligenes xylosoxydans xylosoxydans)
Explore P56547 
Go to UniProtKB:  P56547
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56547
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.67α = 90
b = 54.26β = 95.99
c = 74.55γ = 90
Software Package:
Software NamePurpose
PROCESSdata reduction
AMoREphasing
X-PLORrefinement
PROCESSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance