2PLT | pdb_00002plt

STRUCTURE DETERMINATION OF PLASTOCYANIN FROM A CRYSTAL SPECIMEN WITH HEMIHEDRAL TWINNING FRACTION OF ONE-HALF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 
    0.168 (Depositor) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii.

Redinbo, M.R.Cascio, D.Choukair, M.K.Rice, D.Merchant, S.Yeates, T.O.

(1993) Biochemistry 32: 10560-10567

  • DOI: https://doi.org/10.1021/bi00091a005
  • Primary Citation Related Structures: 
    2PLT

  • PubMed Abstract: 

    The crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii has been determined at 1.5-A resolution with a crystallographic R factor of 16.8%. Plastocyanin is a small (98 amino acids), blue copper-binding protein that catalyzes the transfer of electrons in oxygenic photosynthesis from cytochrome f in the quinol oxidase complex to P700+ in photosystem I. Chlamydomonas reinhardtii plastocyanin is an eight-stranded, antiparallel beta-barrel with a single copper atom coordinated in quasitetrahedral geometry by two imidazole nitrogens (from His-37 and His-87), a cysteine sulfur (from Cys-84), and a methionine sulfur (from Met-92). The molecule contains a region of negative charge surrounding Tyr-83 (the putative distant site of electron transfer) and an exclusively hydrophobic region surrounding His-87; these regions are thought to be involved in the recognition of reaction partners for the purpose of directing electron transfer. Chlamydomonas reinhardtii plastocyanin is similar to the other plastocyanins of known structure, particularly the green algal plastocyanins from Enteromorpha prolifera and Scenedesmus obliquus. A potential "through-bond" path of electron transfer has been identified in the protein that involves the side chain of Tyr-83, the main-chain atoms between residues 83 and 84, the side chain of Cys-84, the copper atom, and the side chain of His-87.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California at Los Angeles, California 90024.

Macromolecule Content 

  • Total Structure Weight: 10.44 kDa 
  • Atom Count: 808 
  • Modeled Residue Count: 98 
  • Deposited Residue Count: 98 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLASTOCYANIN98Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P18068 (Chlamydomonas reinhardtii)
Explore P18068 
Go to UniProtKB:  P18068
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18068
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU

Query on CU



Download:Ideal Coordinates CCD File
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work:  0.168 (Depositor) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.8α = 90
b = 61.8β = 90
c = 25.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    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: 2012-07-18
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Other