1PND

ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.

Fields, B.A.Bartsch, H.H.Bartunik, H.D.Cordes, F.Guss, J.M.Freeman, H.C.

(1994) Acta Crystallogr D Biol Crystallogr 50: 709-730

  • DOI: 10.1107/S0907444994003021
  • Primary Citation of Related Structures:  
    1PND, 1PNC

  • PubMed Abstract: 
  • The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e ...

    The structure of the copper protein plastocyanin from poplar leaves (Populus nigra var. italica) at 173 K has been subjected to two independent refinements, using a single set of synchrotron X-ray data at 1.6 A resolution. Energy-restrained refinement using the program EREF resulted in lower root-mean-square deviations from ideal geometry (e.g. 0.011 A for bond lengths) but a higher residual R (0.153) than restrained least-squares refinement using the program PROLSQ (0.014 A, 0.132). Electron-density difference maps in both refinements provided evidence for disorder at some side chains and solvent atoms, and the PROLSQ refinement made allowance for this disorder. The number of solvent sites identified at the 4sigma(rho) level was 171 in the EREF refinement and 189 in the PROLSQ refinement; 159 of the solvent sites are common to both refinements within 1 A. The root-mean-square differences between the atomic positions produced by the two refinements are 0.08 A for C(alpha) atoms, 0.08 A for backbone atoms and 0.12 A for all non-H atoms (excluding six obvious outliers) of the protein molecule. The two sets of Cu-ligand bond lengths differ by up to 0.07 A, and the ligand-Cu-ligand angles by up to 7 degrees. At 173 K the volume of the unit cell is 4.2% smaller than at 295 K. Greater order in the solvent region is indicated by the location of 79 more solvent sites, the identification of extensive networks of hydrogen-bonded rings of solvent molecules, and a general decrease in the thermal parameters. Within the unit cell, the protein molecules are significantly translated and rotated from their positions at ambient temperature. An important structural change at low temperature is a 180 degrees flip of the peptide group at Ser48-Gly49. Nearly all other significant differences between the structures of the protein at 173 and 295 K occur at exposed side chains. If the backbone atoms in the 173 and 295 K structures are superposed, excluding atoms involved in the peptide flip, the root-mean- square difference between the positions of 393 atoms is 0.25 A. Two internal water molecules, not included in previous descriptions of poplar plastocyanin, have been located. The plastocyanin Cu-site geometry at 173 K is not significantly different from that at 295 K. If plastocyanin undergoes a change in Cu-site geometry at low temperature, as has been suggested on the basis of resonance Raman spectroscopic evidence, then the change is not detected within the limits of precision of the present results.


    Related Citations: 
    • Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 Angstroms Resolution
      Guss, J.M., Bartunik, H.D., Freeman, H.C.
      (1992) Acta Crystallogr B 48: 790
    • Structure of Oxidised Poplar Plastocyanin at 1.6 Angstroms Resolution
      Guss, J.M., Freeman, H.C.
      (1983) J Mol Biol 169: 521
    • X-Ray Crystal Structure Analysis of Plastocyanin at 2.7 Angstroms Resolution
      Colman, P.M., Freeman, H.C., Guss, J.M., Murata, M., Norris, V.A., Ramshaw, J.A.M., Venkatappa, M.P., Freeman, H.C.
      (1978) Nature 272: 319
    • Preliminary Crystallographic Data for a Copper Containing Protein, Plastocyanin
      Chapman, G.V., Colman, P.M., Freeman, H.C., Guss, J.M., Murata, M., Norris, V.A., Ramashaw, J.A.M., Venkatappa, M.P., Freeman, H.C.
      (1977) J Mol Biol 110: 187

    Organizational Affiliation

    Department of Inorganic Chemistry, University of Sydney, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLASTOCYANIN A99Populus nigraMutation(s): 0 
Gene Names: PETE
Find proteins for P00299 (Populus nigra)
Explore P00299 
Go to UniProtKB:  P00299
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.18α = 90
b = 46.29β = 90
c = 56.64γ = 90
Software Package:
Software NamePurpose
EREFrefinement
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-08-08
    Changes: Derived calculations