Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Dihedral - D3  (3D View)
Pseudo Stoichiometry: Homo 12-mer -A12 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78947.25 
• Atom Count: 5522 
• Residue Count: 688 
• Unique protein chains: 3

1B8D

CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN

• DOI: 10.2210/pdb1B8D/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Griffithsia monilis


• Deposited: 1999-01-29 Released: 1999-02-18 
• Deposition Author(s): Ritter, S., Hiller, R.G., Wrench, P.M., Welte, W., Diederichs, K.

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Experimental Data Snapshot

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

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

• PubMed: 10388620 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))	A, K	164	Griffithsia monilis	Mutation(s): 0  Gene Names: cpeA (rpeA)
Find proteins for O36005 (Griffithsia monilis) Go to UniProtKB:  O36005

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))	B, L	177	Griffithsia monilis	Mutation(s): 0  Gene Names: cpeB
Find proteins for O36004 (Griffithsia monilis) Go to UniProtKB:  O36004

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))	G	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PEB	A, B, K, L	PHYCOERYTHROBILIN C33 H40 N4 O6 NKCBCVIFPXGHAV-WAVSMFBNSA-N
PUB	B, L	PHYCOUROBILIN C33 H42 N4 O6 KDCCOOGTVSRCHX-YYVBKQGDSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B, L	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN
UNK	G	L-PEPTIDE LINKING	C4 H9 N O2		--

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 = 187.350	α = 90.00
b = 187.350	β = 90.00
c = 59.310	γ = 120.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	refinement
XSCALE	data scaling
X-PLOR	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-29 
• Released Date: 1999-02-18 
• Deposition Author(s): Ritter, S., Hiller, R.G., Wrench, P.M., Welte, W., Diederichs, K.

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