RCSB PDB - 1EYX: CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS

 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
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PUBClick on this verticalbar to view detailsBest fitted CYCClick on this verticalbar to view detailsBest fitted BLAClick on this verticalbar to view details

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
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  • Reference Sequence
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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
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
R-PHYCOERYTHRINE [auth G],
F [auth H]
6Agarophyton chilenseMutation(s): 0 
Sequence Annotations
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  • 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

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I [auth A]
L [auth B]
M [auth B]
N [auth K]
O [auth K]
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

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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

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PUBClick on this verticalbar to view detailsBest fitted CYCClick on this verticalbar to view detailsBest fitted BLAClick on this verticalbar to view details

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