2V8A | pdb_00002v8a

The structure of Thermosynechococcus elongatus allophycocyanin at 3.5 Angstroems.

PDB DOI: https://doi.org/10.2210/pdb2V8A/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermosynechococcus vestitus BP-1
Mutation(s): No

Deposited: 2007-08-06 Released: 2007-12-11
Deposition Author(s): Murray, J.W., Maghlaoui, K., Barber, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.285 (Depositor), 0.274 (DCC)
R-Value Work:
0.260 (Depositor), 0.241 (DCC)
R-Value Observed:
0.261 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Structure of Allophycocyanin from Thermosynechococcus Elongatus at 3.5 A Resolution.

Murray, J.W., Maghlaoui, K., Barber, J.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 998

PubMed: 18084078 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309107050920
Primary Citation Related Structures:
2V8A

PubMed Abstract:
Cyanobacteria and red algae use light-harvesting pigments bound by proteins to capture solar radiation and to channel excitation energy into their reaction centres. In most cyanobacteria, a multi-megadalton soluble structure known as the phycobilisome is a major light-harvesting system. Allophycocyanin is the main component of the phycobilisome core, forming a link between the rest of the phycobilisome and the reaction-centre core. The crystal structure of allophycocyanin from Thermosynechococcus elongatus (TeAPC) has been determined and refined at 3.5 A resolution to a crystallographic R value of 26.0% (R(free) = 28.5%). The structure was solved by molecular replacement using the allophycocyanin structure from Spirulina platensis as the search model. The asymmetric unit contains an (alphabeta) monomer which is expanded by symmetry to a crystallographic trimer.

Organizational Affiliation

Division of Molecular Biosciences, Imperial College, Exhibition Road, London SW7 2AZ, England.

Macromolecule Content

Total Structure Weight: 36.12 kDa
Atom Count: 2,523
Modeled Residue Count: 321
Deposited Residue Count: 322
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLOPHYCOCYANIN ALPHA CHAIN	A	161	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P50030 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P50030 Go to UniProtKB: P50030
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50030
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLOPHYCOCYANIN BETA CHAIN	B	161	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P50031 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P50031 Go to UniProtKB: P50031
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 3.50 Å
R-Value Free: 0.285 (Depositor), 0.274 (DCC)
R-Value Work: 0.260 (Depositor), 0.241 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.177	α = 90
b = 102.177	β = 90
c = 193.984	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Murray, J.W.

Maghlaoui, K.

Barber, J.

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description