1PLC

ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution.

Guss, J.M.Bartunik, H.D.Freeman, H.C.

(1992) Acta Crystallogr.,Sect.B 48: 790-811


  • PubMed Abstract: 
  • The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = ...

    The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = 46.86 (3), c = 57.60 (3) A. The 14,303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 A and the root-mean-square difference between the positions of the C alpha atoms in this refined model and in the structure previously refined at 1.6 A resolution is 0.11 A. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A.


    Related Citations: 
    • 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.,Ramshaw, J.A.M.,Venkatappa, M.P.
      (1977) J.Mol.Biol. 110: 187
    • 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


    Organizational Affiliation

    Department of Inorganic Chemistry, University of Sydney, NSW, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 29.600α = 90.00
b = 46.860β = 90.00
c = 57.600γ = 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: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other