1B8D

CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution.

Ritter, S.Hiller, R.G.Wrench, P.M.Welte, W.Diederichs, K.

(1999) J.Struct.Biol. 126: 86-97

  • DOI: 10.1006/jsbi.1999.4106

  • PubMed Abstract: 
  • The structure of R-phycoerythrin (R-PE) from the red alga Griffithsia monilis was solved at 1.90-A resolution by molecular replacement, using the atomic coordinates of cyanobacterial phycocyanin from Fremyella diplosiphon as a model. The crystallogra ...

    The structure of R-phycoerythrin (R-PE) from the red alga Griffithsia monilis was solved at 1.90-A resolution by molecular replacement, using the atomic coordinates of cyanobacterial phycocyanin from Fremyella diplosiphon as a model. The crystallographic R factor for the final model is 17.5% (Rfree 22.7%) for reflections in the range 100-1.90 A. The model consists of an (alphabeta)2 dimer with an internal noncrystallographic dyad and a fragment of the gamma-polypeptide. The alpha-polypeptide (164 amino acid residues) has two covalently bound phycoerythrobilins at positions alpha82 and alpha139. The beta-polypeptide (177 residues) has two phycoerythrobilins bound to residues beta82 and beta158 and one phycourobilin covalently attached to rings A and D at residues beta50 and beta61, respectively. The electron density of the gamma-polypeptide is mostly averaged out by threefold crystallographic symmetry, but a dipeptide (Gly-Tyr) and one single Tyr could be modeled. These two tyrosine residues of the gamma-polypeptide are in close proximity to the phycoerythrobilins at position beta82 of two symmetry-related beta-polypeptides and are related by the same noncrystallographic dyad as the (alphabeta)2 dimer. Possible energy transfer pathways are discussed briefly.


    Organizational Affiliation

    Institut für Biophysik und Strahlenbiologie, Universität Freiburg, Albertstrasse 23, Freiburg, D-79104, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
A, K
164Griffithsia monilisMutation(s): 0 
Gene Names: cpeA (rpeA)
Find proteins for O36005 (Griffithsia monilis)
Go to UniProtKB:  O36005
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
B, L
177Griffithsia monilisMutation(s): 0 
Gene Names: cpeB
Find proteins for O36004 (Griffithsia monilis)
Go to UniProtKB:  O36004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
G
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download SDF File 
Download CCD File 
A, B, K, L
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, L
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 187.350α = 90.00
b = 187.350β = 90.00
c = 59.310γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
XSCALEdata scaling
X-PLORmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance