1A8Z

STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of a 16.8 kDa copper protein at 2.1 A resolution using anomalous scattering data with direct methods.

Harvey, I.Hao, Q.Duke, E.M.Ingledew, W.J.Hasnain, S.S.

(1998) Acta Crystallogr.,Sect.D 54: 629-635


  • PubMed Abstract: 
  • The structure of rusticyanin, an acid-stable copper protein, has been determined at 2.1 A resolution by direct methods combined with the single-wavelength anomalous scattering (SAS) of copper (f" = 3.9 e-) and then conventionally refined (Rcryst = 18 ...

    The structure of rusticyanin, an acid-stable copper protein, has been determined at 2.1 A resolution by direct methods combined with the single-wavelength anomalous scattering (SAS) of copper (f" = 3.9 e-) and then conventionally refined (Rcryst = 18.7%, Rfree = 21.9%). This is the largest unknown protein structure (Mr approximately /= 16.8 kDa) to be determined using the SAS and direct-methods approach and demonstrates that by exploiting the anomalous signal at a single wavelength, direct methods can be used to determine phases at typical (approximately 2 A) macromolecular crystallographic resolutions. Extrapolating from the size of the anomalous signal for copper (f" approximately 4 e-), this result suggests that the approach could be used for proteins with molecular weights of up to 33 kDa per Se (f"max++ = 8 e- at the 'white line') and 80 kDa for a Pt derivative (f"max = 19 e- at the 'white line', L3 edge). The method provides a powerful alternative in solving a de novo protein structure without either preparing multiple crystals (i.e. isomorphous heavy-atom derivative plus native crystals) or collecting multi-wavelength anomalous diffraction (MAD) data.


    Related Citations: 
    • Complete 13C Assignments for Recombinant Cu(I) Rusticyanin. Prediction of Secondary Structure from Patterns of Chemical Shifts
      Toy-Palmer, A.,Prytulla, S.,Dyson, H.J.
      (1995) FEBS Lett. 365: 35
    • Copper Protein Structures
      Adman, E.T.
      (1991) Adv.Protein Chem. 43: 145
    • The Respiratory Chain of Thiobacillus Ferrooxidans: The Reduction of Cytochromes by Fe2+ and the Preliminary Characterization of Rusticyanin a Novel "Blue" Copper Protein
      Cobley, J.G.,Haddock, B.A.
      (1975) FEBS Lett. 60: 29
    • Oasis-A Computer Program for Breaking the Phase Ambiguity in Oas or Sir Protein Data
      Hao, Q.,Gu, Y.X.,Zheng, C.D.,Fan, H.F.
      () TO BE PUBLISHED --: --
    • X-Ray Absorption Studies and Homology Modeling Define the Structural Features that Specify the Nature of the Copper Site in Rusticyanin
      Grossmann, J.G.,Ingledew, W.J.,Harvey, I.,Strange, R.W.,Hasnain, S.S.
      (1995) Biochemistry 34: 8406
    • Multiple Wavelength Anomalous Diffraction (MAD) Crystal Structure of Rusticyanin: A Highly Oxidizing Cupredoxin with Extreme Acid Stability
      Walter, R.L.,Ealick, S.E.,Friedman, A.M.,Blake II, R.C.,Proctor, P.,Shoham, M.
      (1996) J.Mol.Biol. 263: 730
    • Crystallization and Preliminary X-Ray Crystallographic Studies of Rusticyanin from Thiobacillus Ferrooxidans
      Djebli, A.,Proctor, P.,Blake II, R.C.,Shoham, M.
      (1992) J.Mol.Biol. 227: 581
    • The Purification and Some Properties of Rusticyanin, a Blue Copper Protein Involved in Iron(II) Oxidation from Thiobacillus Ferro-Oxidans
      Cox, J.C.,Boxer, D.H.
      (1978) Biochem.J. 174: 497
    • Amino Acid Sequence of the Blue Copper Protein Rusticyanin from Thiobacillus Ferrooxidans
      Ronk, M.,Shively, J.E.,Shute, E.A.,Blake II, R.C.
      (1991) Biochemistry 30: 9435


    Organizational Affiliation

    School of Applied Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, England, and CLRC Daresbury Laboratory, Warrington WA4 4AD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUSTICYANIN
A
153Acidithiobacillus ferrooxidansGene Names: rus (rusTA)
Find proteins for P0C918 (Acidithiobacillus ferrooxidans)
Go to UniProtKB:  P0C918
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.430α = 90.00
b = 60.680β = 107.82
c = 38.010γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance