2GIM

1.6 Angstrom structure of plastocyanin from Anabaena variabilis

• PDB DOI: https://doi.org/10.2210/pdb2GIM/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Trichormus variabilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-29 Released: 2006-04-11 
• Deposition Author(s): Schmidt, L., Harris, P., Christensen, H.E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Structure of plastocyanin from the cyanobacterium Anabaena variabilis.

Schmidt, L., Christensen, H.E., Harris, P.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1022-1029

• PubMed: 16929103 
• DOI: https://doi.org/10.1107/S0907444906023638
• Primary Citation of Related Structures:  
  2GIM


• PubMed Abstract: 
  

  Plastocyanin from the cyanobacterium Anabaena variabilis was heterologously produced in Escherichia coli and purified. Plate-like crystals were obtained by crystallization in 1.15 M trisodium citrate and 7.67 mM sodium borate buffer pH 8.5. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 67.85, b = 45.81, c = 63.41 Angstrom. The structure of the oxidized protein was solved to a resolution of 1.6 Angstrom using plastocyanin from Phormidium laminosum as a search model. Two molecules were found in the asymmetric unit. The electrostatic surface of the basic protein showed a large population of positively charged residues in the northern site, whereas the eastern site lacked the two strongly negatively charged patches. The copper ion was found to be relatively mobile and there were two distinct conformations of His61.

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Organizational Affiliation: 

Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.62 kDa 
• Atom Count: 1,917 
• Modelled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastocyanin	A, B [auth C]	106	Trichormus variabilis	Mutation(s): 0  Gene Names: petE
UniProt
Find proteins for P0C178 (Anabaena variabilis) Explore P0C178  Go to UniProtKB:  P0C178

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.85	α = 90
b = 45.81	β = 90
c = 63.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Schmidt, L., Harris, P., Christensen, H.E.M.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description