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 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1PCS

  • 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 A42D/D47P/A63L, which are stable for days in its oxidized form, were grown from ammonium sulfate, with the cell constants a = b = 34 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PLASTOCYANINA98Synechocystis sp. PCC 6803Mutation(s): 3 
UniProt
Find proteins for P21697 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P21697 
Go to UniProtKB:  P21697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21697
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth 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 
  • R-Value Observed: 0.167 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.3α = 90
b = 34.3β = 90
c = 111.8γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations