2W88

Plastocyanin variant with N-terminal Methionine - open structure

• PDB DOI: https://doi.org/10.2210/pdb2W88/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Leptolyngbya laminosa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-01-14 Released: 2009-10-27 
• Deposition Author(s): Crowley, P.B., Matias, P.M., Khan, A.R.

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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

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

• PubMed: 19834935 
• 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.

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Organizational Affiliation: 

UCD Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35.34 kDa 
• Atom Count: 2,449 
• Modelled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASTOCYANIN	A, B, C	106	Leptolyngbya laminosa	Mutation(s): 0
UniProt
Find proteins for Q51883 (Phormidium laminosum) Explore Q51883  Go to UniProtKB:  Q51883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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	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 = 127.7	α = 90
b = 127.7	β = 90
c = 94.99	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Crowley, P.B., Matias, P.M., Khan, A.R.

Revision History  

• 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