2W88

Plastocyanin variant with N-terminal Methionine - open structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Metal-Mediated Self-Assembly of a Beta-Sandwich Protein.

Crowley, P.B., Matias, P.M., Khan, A.R., Roessle, M., Svergun, D.I.

(2009) Chemistry 15: 12672

  • DOI: https://doi.org/10.1002/chem.200901410
  • Primary Citation of Related Structures:  
    2W88, 2W8C

  • PubMed Abstract: 

    The beta-sandwich cupredoxin Plastocyanin (Pc) was found to self-assemble in the presence of Zn(2+), a known mediator of protein-protein interfaces. Diffraction-quality crystals of Pc grew from solutions containing zinc acetate as the sole precipitant. Di- and trinuclear zinc sites contribute to the crystal contacts in this structure. A different crystal form, also involving numerous zinc bridging ions, was obtained in the presence of poly(ethylene glycol) 8 000. Comparison of the two crystal forms reveals the effect of macromolecular crowding on self-assembly. Solution-state structural characterisation of the Zn(2+)-mediated Pc oligomers was performed by using a combination of chemical shift perturbation mapping and small-angle X-ray scattering. The data indicate the formation of dimers in solution. The implications for metal-mediated assembly and crystallisation are discussed.

    • Organizational Affiliation: 

    UCD Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland. [email protected]


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLASTOCYANIN
A, B, C
106Leptolyngbya laminosaMutation(s): 0 
UniProt
Find proteins for Q51883 (Phormidium laminosum)
Explore Q51883 
Go to UniProtKB:  Q51883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51883
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
M [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.7α = 90
b = 127.7β = 90
c = 94.99γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Database references
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description