5NB3

High resolution C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM.

Sonani, R.R.Roszak, A.W.Ortmann de Percin Northumberland, C.Madamwar, D.Cogdell, R.J.

(2018) Photosyn. Res. 135: 65-78

  • DOI: 10.1007/s11120-017-0443-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-h ...

    C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94-103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB's spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17-28, 2016).


    Organizational Affiliation

    Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388315, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
A, B, C, D, E, F, G, H, I, J, K, L
164Phormidium rubidum A09DMMutation(s): 0 
Gene Names: cpeA
Find proteins for A0A0E3W010 (Phormidium rubidum A09DM)
Go to UniProtKB:  A0A0E3W010
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
M, N, O, P, Q, R, S, T, U, V, W, X
184Phormidium rubidum A09DMMutation(s): 0 
Gene Names: cpeB
Find proteins for A0A0E4G455 (Phormidium rubidum A09DM)
Go to UniProtKB:  A0A0E4G455
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, N, P, Q, R, V
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A, C, H, J, K, N, O, P, Q, U, V, W
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, I, J, L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
T, V
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
M, N, O, P, Q, R, S, U, W, X
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
M, N, O, P, Q, R, S, T, U, V, W, X
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.155 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 110.046α = 78.76
b = 110.170β = 82.28
c = 118.516γ = 60.43
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of EnergyUnited StatesDE-SC0001035

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references