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
  • R-Value Observed: 0.150 

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This is version 1.4 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 B 48: 790-811

  • DOI: https://doi.org/10.1107/s0108768192004270
  • Primary Citation of Related Structures:  
    1PLC

  • 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 = 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLASTOCYANIN99Populus nigraMutation(s): 0 
UniProt
Find proteins for P00299 (Populus nigra)
Explore P00299 
Go to UniProtKB:  P00299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00299
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.6α = 90
b = 46.86β = 90
c = 57.6γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations