3PCY

THE CRYSTAL STRUCTURE OF MERCURY-SUBSTITUTED POPLAR PLASTOCYANIN AT 1.9-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of mercury-substituted poplar plastocyanin at 1.9-A resolution.

Church, W.B.Guss, J.M.Potter, J.J.Freeman, H.C.

(1986) J.Biol.Chem. 261: 234-237


  • PubMed Abstract: 
  • The crystal structure of Hg(II)-plastocyanin has been determined and refined at a resolution of 1.9 A. The crystals were prepared by soaking crystals of Cu(II)-plastocyanin from poplar leaves (Populus nigra var. italica) in a solution of a mercuric s ...

    The crystal structure of Hg(II)-plastocyanin has been determined and refined at a resolution of 1.9 A. The crystals were prepared by soaking crystals of Cu(II)-plastocyanin from poplar leaves (Populus nigra var. italica) in a solution of a mercuric salt. Replacement of the Cu(II) atom in plastocyanin by Hg(II) causes only minor changes in the geometry of the metal site, and there are few significant changes elsewhere in the molecule. It is concluded that, as in the case of the native protein, the geometry of the metal site is determined by the polypeptide. The weak metal-S(methionine) bond found in Cu(II)-plastocyanin remains weak in Hg(II)-plastocyanin. The "flip" of a proline side chain close to the metal site from a C gamma-exo conformation in Cu(II)-plastocyanin to a C gamma-endo conformation in Hg(II)-plastocyanin suggests that this region of the molecule is particularly flexible. Crystallographic evidence for the close similarity of the Hg(II)- and Cu(II)-plastocyanin structures was originally obtained from electron density difference maps at 2.5-A resolution. The refinement of the structure was begun with a set of atomic coordinates taken from the structure of Cu(II)-plastocyanin. A Hg(II) atom was substituted for the Cu(II) atom, and the side chains of 6 residues in the vicinity of the metal site were omitted. Three series of stereochemically restrained least-squares refinement calculations were interspersed with two stages of model adjustment followed by phase extension. Fifty-nine water molecules were located. The final structure has a crystallographic residual R = 0.16.


    Related Citations: 
    • The Crystal Structure of Poplar Apoplastocyanin at 1.8-Angstroms Resolution. The Geometry of the Copper-Binding Site is Created by the Polypeptide
      Garrett, T.P.J.,Clingeleffer, D.J.,Guss, J.M.,Rogers, S.J.,Freeman, H.C.
      (1984) J.Biol.Chem. 259: 2822
    • 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.
      (1978) Nature 272: 319
    • Structure of Oxidized Poplar Plastocyanin at 1.6 Angstroms Resolution
      Guss, J.M.,Freeman, H.C.
      (1983) J.Mol.Biol. 169: 521



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASTOCYANIN
A
99Populus nigraMutation(s): 0 
Gene Names: PETE
Find proteins for P00299 (Populus nigra)
Go to UniProtKB:  P00299
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 29.830α = 90.00
b = 46.650β = 90.00
c = 57.750γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-01-21
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other