1JXG | pdb_00001jxg

The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge

• PDB DOI: https://doi.org/10.2210/pdb1JXG/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Populus nigra
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-09-07 Released: 2001-12-19 
• Deposition Author(s): Milani, M., Andolfi, L., Cannistraro, S., Verbeet, M.P., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.205 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.145 (Depositor) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

The 1.6 A resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge.

Milani, M., Andolfi, L., Cannistraro, S., Verbeet, M.P., Bolognesi, M.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1735-1738

• PubMed: 11679761 
• DOI: https://doi.org/10.1107/s0907444901013221
• Primary Citation Related Structures: 
  1JXG


• PubMed Abstract: 
  

  Plastocyanin is an electron-transfer protein which has been largely used for biophysical studies as well as for protein-engineering experiments. A surface disulfide bridge has been engineered in poplar plastocyanin to allow protein chemisorption on gold substrates. The mutated plastocyanin crystal structure has been studied at 1.6 A resolution (R factor = 0.145, R(free) = 0.205) to characterize the effects of the engineered disulfide on the overall protein structure and on the Cu-coordination sphere in view of biophysical applications. The new orthorhombic crystal form isolated for the mutated plastocyanin displays two protein molecules per asymmetric unit.

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Organizational Affiliation: 
• Department of Physics-INFM, c/o Advanced Biotechnology Center-IST, University of Genova, Largo Rosanna Benzi 10, 16132 Genova, Italy.

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: 21.4 kDa 
• Atom Count: 1,781 
• Modeled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASTOCYANIN A	A, B	100	Populus nigra	Mutation(s): 2
UniProt
Find proteins for P00299 (Populus nigra) Explore P00299  Go to UniProtKB:  P00299

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU1	C [auth A], D [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.205 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.145 (Depositor) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.381	α = 90
b = 49.306	β = 90
c = 76.576	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-19 
Deposition Author(s): Milani, M., Andolfi, L., Cannistraro, S., Verbeet, M.P., Bolognesi, M.

Revision History  

• Version 1.0: 2001-12-19
  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: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary