1PCS

THE 2.15 A CRYSTAL STRUCTURE OF A TRIPLE MUTANT PLASTOCYANIN FROM THE CYANOBACTERIUM SYNECHOCYSTIS SP. PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.15 A crystal structure of a triple mutant plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803.

Romero, A.De la Cerda, B.Varela, P.F.Navarro, J.A.Hervas, M.De la Rosa, M.A.

(1998) J.Mol.Biol. 275: 327-336

  • DOI: 10.1006/jmbi.1997.1455

  • PubMed Abstract: 
  • The crystal structure of the triple mutant A42D/D47P/A63L plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803 has been determined by Patterson search methods using the known structure of the poplar protein. Crystals of the triple mutant A ...

    The crystal structure of the triple mutant A42D/D47P/A63L plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803 has been determined by Patterson search methods using the known structure of the poplar protein. Crystals of the triple mutant A42D/D47P/A63L, which are stable for days in its oxidized form, were grown from ammonium sulfate, with the cell constants a = b = 34.3 A and c = 111.8 A belonging to space group P3(2)21. The structure was refined using restrained crystallographic refinement to an R-factor of 16.7% for 4070 independent reflections between 8.0 and 2.15 A with intensities greater than 2 sigma (I), with root mean square deviations of 0.013 A and 1.63 degrees from ideal bond lengths and bond angles, respectively. The final model comprises 727 non-hydrogen protein atoms within 98 residues, 75 water molecules and a single copper ion. The overall tertiary fold of Synechocystis plastocyanin consists of a compact ellipsoidal beta-sandwich structure made up of two beta-sheets embracing a hydrophobic core. Each sheet contains parallel and antiparallel beta-strands. In addition to the beta-sheets, the structure contains an alpha-helix from Pro47 to Lys54 that follows beta-strand 4. The three-dimensional structure of Synechocystis plastocyanin is thus similar to those reported for the copper protein isolated from eukaryotic organisms and, in particular, from the cyanobacterium Anabaena variabilis, the only cyanobacterial plastocyanin structure available so far. The molecule holds an hydrophobic region surrounding His87, as do other plastocyanins, but the lack of negatively charged residues at the putative distant remote site surrounding Tyr83 could explain why the Synechocystis protein exhibits a collisional reaction mechanism for electron transfer to photosystem I (PSI), which involves no formation of the transient plastocyanin-PSI complex kinetically observed in green algae and higher plants.


    Related Citations: 
    • Solution Structure of Reduced Plastocyanin from the Blue-Green Alga Anabaena Variabilis
      Badsberg, U.,Jorgensen, A.M.,Gesmar, H.,Led, J.J.,Hammerstad, J.M.,Jespersen, L.L.,Ulstrup, J.
      (1996) Biochemistry 35: 7021
    • Structure of Oxidized Poplar Plastocyanin at 1.6 A Resolution
      Guss, J.M.,Freeman, H.C.
      (1983) J.Mol.Biol. 169: 521


    Organizational Affiliation

    Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASTOCYANIN
A
98Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 3 
Gene Names: petE
Find proteins for P21697 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P21697
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.167 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 34.300α = 90.00
b = 34.300β = 90.00
c = 111.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
CCP4data scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance