1BYP | pdb_00001byp

E43K,D44K DOUBLE MUTANT PLASTOCYANIN FROM SILENE

• PDB DOI: https://doi.org/10.2210/pdb1BYP/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Silene latifolia subsp. alba
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-10-19 Released: 1999-10-19 
• Deposition Author(s): Sugawara, H., Inoue, T., Li, C., Gotowda, M., Hibino, T., Takabe, T., Kai, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of wild-type and mutant plastocyanins from a higher plant, Silene.

Sugawara, H., Inoue, T., Li, C., Gotowda, M., Hibino, T., Takabe, T., Kai, Y.

(1999) J Biochem 125: 899-903

• PubMed: 10220581 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a022366
• Primary Citation Related Structures: 
  1BYO, 1BYP


• PubMed Abstract: 
  

  Plastocyanin functions as an electron carrier between the cytochrome b6f complex and photosystem I. The crystal structures of the wild-type and E43K/D44K double mutant from the higher plant, Silene, have been determined at 2.0 and 1.75 A resolution, respectively. The wild-type plastocyanin comprises two monomers per asymmetric unit, one of which shows the unusually great distance between the copper ion and the Ndelta1 atom of H87 because of the hydrogen bond network formation between H87 and symmetry-related G10. The root mean square deviation for Ca atoms between the wild-type and mutant plastocyanins is 0.44 A, however, the electrostatic potential maps of their molecular surfaces are remarkably different. The low electron-transfer rate in the E43K/D44K mutant results from the hindrance of electrostatic interactions, not from the structural change due to the mutation.

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Organizational Affiliation: 
• Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.48 kDa 
• Atom Count: 806 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PLASTOCYANIN)	A	99	Silene latifolia subsp. alba	Mutation(s): 2
UniProt
Find proteins for P07030 (Silene latifolia subsp. alba) Explore P07030  Go to UniProtKB:  P07030

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: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.9	α = 90
b = 55.9	β = 90
c = 68.2	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-19 
Deposition Author(s): Sugawara, H., Inoue, T., Li, C., Gotowda, M., Hibino, T., Takabe, T., Kai, Y.

Revision History  

• Version 1.0: 1999-10-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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: 2023-08-09
  Changes: Data collection, Refinement description