1EYX

CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.279 
  • R-Value Observed: 0.192 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.

Contreras-Martel, C.Martinez-Oyanedel, J.Bunster, M.Legrand, P.Piras, C.Vernede, X.Fontecilla-Camps, J.C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 52-60

  • DOI: https://doi.org/10.1107/s0907444900015274
  • Primary Citation of Related Structures:  
    1EYX

  • PubMed Abstract: 

    R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 A resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final R(work) and R(free) factors are 0.16 and 0.25, respectively. All the residues and chromophores of the alpha- and beta-chains are well defined in the electron-density maps. Some residues belonging to the gamma-linker are also recognizable.


  • Organizational Affiliation

    Laboratorio de Biofísica Molecular, Departamento de Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R-PHYCOERYTHRINA,
C [auth K]
164Agarophyton chilenseMutation(s): 0 
UniProt
Find proteins for Q7SIG0 (Agarophyton chilense)
Explore Q7SIG0 
Go to UniProtKB:  Q7SIG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIG0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
R-PHYCOERYTHRINB,
D [auth L]
177Agarophyton chilenseMutation(s): 0 
UniProt
Find proteins for Q7SIF9 (Agarophyton chilense)
Explore Q7SIF9 
Go to UniProtKB:  Q7SIF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF9
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
R-PHYCOERYTHRINE [auth G],
F [auth H]
6Agarophyton chilenseMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PUB
Query on PUB

Download Ideal Coordinates CCD File 
K [auth B],
P [auth L]
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
CYC
Query on CYC

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth B]
N [auth K]
O [auth K]
I [auth A],
L [auth B],
M [auth B],
N [auth K],
O [auth K],
Q [auth L],
R [auth L]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
BLA
Query on BLA

Download Ideal Coordinates CCD File 
H [auth A]BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B,
D [auth L]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.279 
  • R-Value Observed: 0.192 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.268α = 90
b = 187.268β = 90
c = 59.109γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-22
    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: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description