1AG6 | pdb_00001ag6

PLASTOCYANIN FROM SPINACH

• PDB DOI: https://doi.org/10.2210/pdb1AG6/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Spinacia oleracea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1997-04-02 Released: 1998-10-21 
• Deposition Author(s): Xue, Y., Okvist, M., Young, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spinach plastocyanin at 1.7 A resolution.

Xue, Y., Okvist, M., Hansson, O., Young, S.

(1998) Protein Sci 7: 2099-2105

• PubMed: 9792096 
• DOI: https://doi.org/10.1002/pro.5560071006
• Primary Citation Related Structures: 
  1AG6


• PubMed Abstract: 
  

  The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins.

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Organizational Affiliation: 
• Department of Chemistry, Biochemistry and Biophysics, Göteborg University, Sweden. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.54 kDa 
• Atom Count: 802 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASTOCYANIN	A	99	Spinacia oleracea	Mutation(s): 1
UniProt
Find proteins for P00289 (Spinacia oleracea) Explore P00289  Go to UniProtKB:  P00289

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.191 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.582	α = 90
b = 75.582	β = 90
c = 32.707	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-21 
Deposition Author(s): Xue, Y., Okvist, M., Young, S.

Revision History  

• Version 1.0: 1998-10-21
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-02
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection