6XWK | pdb_00006xwk

Crystal structure of Phormidium rubidum phycocyanin

• PDB DOI: https://doi.org/10.2210/pdb6XWK/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Phormidium rubidum A09DM
• Mutation(s): No 


• Deposited: 2020-01-23 Released: 2020-04-29 
• Deposition Author(s): Sonani, R.R., Roszak, A.W., Cogdell, R.J., Madamwar, D., Liu, H., Gross, M.L., Blankenship, R.E.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.145 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 

Starting Model: experimental

Literature

Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin.

Sonani, R.R., Roszak, A.W., Liu, H., Gross, M.L., Blankenship, R.E., Madamwar, D., Cogdell, R.J.

(2020) Photosynth Res 144: 349-360

• PubMed: 32303893 
• DOI: https://doi.org/10.1007/s11120-020-00746-7
• Primary Citation Related Structures: 
  6XWK


• PubMed Abstract: 
  

  The crystal structure of phycocyanin (pr-PC) isolated from Phormidium rubidum A09DM (P. rubidum) is described at a resolution of 1.17 Å. Electron density maps derived from crystallographic data showed many clear differences in amino acid sequences when compared with the previously obtained gene-derived sequences. The differences were found in 57 positions (30 in α-subunit and 27 in β-subunit of pr-PC), in which all residues except one (β145Arg) are not interacting with the three phycocyanobilin chromophores. Highly purified pr-PC was then sequenced by mass spectrometry (MS) using LC-MS/MS. The MS data were analyzed using two independent proteomic search engines. As a result of this analysis, complete agreement between the polypeptide sequences and the electron density maps was obtained. We attribute the difference to multiple genes in the bacterium encoding the phycocyanin apoproteins and that the gene sequencing sequenced the wrong ones. We are not implying that protein sequencing by mass spectrometry is more accurate than that of gene sequencing. The final 1.17 Å structure of pr-PC allows the chromophore interactions with the protein to be described with high accuracy.

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Organizational Affiliation: 
• Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India.
Małopolska Centre of Biotechnology, Jagiellonian University, 30-387, Kraków, Poland.
Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK. [e-mail].
Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA.
Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India. [e-mail].
Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.15 kDa 
• Atom Count: 3,359 
• Modeled Residue Count: 334 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin alpha subunit	A [auth AAA]	162	Phormidium rubidum A09DM	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin beta subunit	B [auth BBB]	172	Phormidium rubidum A09DM	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	C [auth AAA], M [auth BBB], N [auth BBB]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N
PGE	O [auth BBB]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth AAA]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD	J [auth AAA], K [auth AAA], P [auth BBB], Q [auth BBB]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], L [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B [auth BBB]	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free:  0.145 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.32	α = 90
b = 106.32	β = 90
c = 58.67	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Sonani, R.R., Roszak, A.W., Cogdell, R.J., Madamwar, D., Liu, H., Gross, M.L., Blankenship, R.E.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001035

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description