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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 57: 52-60


  • 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. Th ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R-PHYCOERYTHRIN
A, K
164Gracilaria chilensisGene Names: rpeA
Find proteins for Q7SIG0 (Gracilaria chilensis)
Go to UniProtKB:  Q7SIG0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R-PHYCOERYTHRIN
B, L
177Gracilaria chilensisGene Names: rpeB
Find proteins for Q7SIF9 (Gracilaria chilensis)
Go to UniProtKB:  Q7SIF9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
R-PHYCOERYTHRIN
G, H
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CYC
Query on CYC

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

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Download CCD File 
B, L
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
 Ligand Interaction
BLA
Query on BLA

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Download CCD File 
A
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, 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 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 187.268α = 90.00
b = 187.268β = 90.00
c = 59.109γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXL-97refinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance