4GXE | pdb_00004gxe

T. vulcanus Phycocyanin crystallized in 4M Urea

PDB DOI: https://doi.org/10.2210/pdb4GXE/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Thermostichus vulcanus
Mutation(s): No

Deposited: 2012-09-04 Released: 2013-03-06
Deposition Author(s): Marx, A., Adir, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.299 (Depositor), 0.244 (DCC)
R-Value Work:
0.255 (Depositor), 0.246 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

Marx, A., Adir, N.

(2013) Biochim Biophys Acta 1827: 311-318

PubMed: 23201474 Search on PubMed
DOI: https://doi.org/10.1016/j.bbabio.2012.11.006
Primary Citation Related Structures:
4F0T, 4F0U, 4GXE, 4GY3, 4H0M

PubMed Abstract:
X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.

Organizational Affiliation

Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.

Macromolecule Content

Total Structure Weight: 37.87 kDa
Atom Count: 2,701
Modeled Residue Count: 334
Deposited Residue Count: 334
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-phycocyanin alpha subunit	A	162	Thermostichus vulcanus	Mutation(s): 0
UniProt
Find proteins for Q9AM02 (Thermostichus vulcanus) Explore Q9AM02 Go to UniProtKB: Q9AM02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9AM02
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-phycocyanin beta subunit	B	172	Thermostichus vulcanus	Mutation(s): 0
UniProt
Find proteins for Q71RW8 (Thermostichus vulcanus) Explore Q71RW8 Go to UniProtKB: Q71RW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71RW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B], H [auth B]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]
URE Query on URE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	B	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.299 (Depositor), 0.244 (DCC)
R-Value Work: 0.255 (Depositor), 0.246 (DCC)
R-Value Observed: 0.255 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.75	α = 90
b = 153.75	β = 90
c = 39.72	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Marx, A.

Adir, N.

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2013-03-27
Changes: Other
Version 1.2: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description