1LIA

CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA AT 2.8 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of R-phycoerythrin from Polysiphonia urceolata at 2.8 A resolution.

Chang, W.R.Jiang, T.Wan, Z.L.Zhang, J.P.Yang, Z.X.Liang, D.C.

(1996) J.Mol.Biol. 262: 721-731

  • DOI: 10.1006/jmbi.1996.0547

  • PubMed Abstract: 
  • The structure of R-phycoerythrin (R-PE) from Polysiphonia urceolata was determined at 2.8 A resolution. The crystals belong to space group R3 with unit cell dimensions of a = b = 189.8 A, c = 60.1 A. The subunit composition of R-PE is (alpha 2 beta 2 ...

    The structure of R-phycoerythrin (R-PE) from Polysiphonia urceolata was determined at 2.8 A resolution. The crystals belong to space group R3 with unit cell dimensions of a = b = 189.8 A, c = 60.1 A. The subunit composition of R-PE is (alpha 2 beta 2)3 gamma. The three-dimensional structure of R-PE was solved by the multiple isomorphous replacement method. After several cycles of model building and refinement, the crystallographic R-factor of the final model is 18.0% with data from 10.0 to 2.8 A resolution. The four phycoerythrobilin chromophores alpha 84, alpha 140a, beta 84 and beta 155 in an (alpha beta) unit are each covalently bound to a cysteine residue through ring A. The phycourobilin chromophore is bound to cysteine beta 50 by ring A and bound to cysteine beta 61 by ring D. The ring A and ring D of phycourobilin deviate from the conjugate plane formed by ring B and ring C and the four rings form a boat-shaped structure. R-PE contains a 34 kDa gamma subunit that is assumed to lie in the central channel of the molecular disc (alpha 2 beta 2)3. The energy transfer and relationship between cysteine residues and chromophores are discussed.


    Related Citations: 
    • Crystal Structure of R-Phycoerythrin from Polysiphonia Urceolata at 0.5Nm Resolution
      Chang, W.R.,Wan, Z.L.,Jiang, T.,Zhang, J.P.,Song, H.W.,Wang, S.G.,Gui, L.L.,Liang, D.C.,Zhu, J.C.,Yang, Z.X.
      (1995) Prog.Nat.Sci. 5: 202


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R-PHYCOERYTHRIN
A, K
164Polysiphonia urceolataGene Names: cpeA (rpeA)
Find proteins for P84861 (Polysiphonia urceolata)
Go to UniProtKB:  P84861
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R-PHYCOERYTHRIN
B, L
177Polysiphonia urceolataGene Names: cpeB (rpeB)
Find proteins for P84862 (Polysiphonia urceolata)
Go to UniProtKB:  P84862
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download SDF File 
Download CCD File 
A, B, K, L
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
PUB
Query on PUB

Download SDF File 
Download CCD File 
B, L
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.180 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 189.800α = 90.00
b = 189.800β = 90.00
c = 60.100γ = 120.00
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance