1B33 | pdb_00001b33

STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8

PDB DOI: https://doi.org/10.2210/pdb1B33/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Mastigocladus laminosus
Mutation(s): Yes

Deposited: 1998-12-15 Released: 1999-02-23
Deposition Author(s): Reuter, W., Wiegand, G., Huber, R., Than, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.256 (Depositor)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus.

Reuter, W., Wiegand, G., Huber, R., Than, M.E.

(1999) Proc Natl Acad Sci U S A 96: 1363-1368

PubMed: 9990029 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.96.4.1363
Primary Citation Related Structures:
1B33

PubMed Abstract:
An electrophoretically purified allophycocyanin-linker complex, AP. LC7.8, from phycobilisomes of Mastigocladus laminosus has been crystallized in the orthorhombic space group P212121. Cryocrystallographic x-ray measurements enabled the structural analysis of the complex at a resolution of 2.2 A. The asymmetric unit contains two side-to-side associated "trimeric" (alphabeta)3 allophycocyanin complexes comprising the linker polypeptide in a defined orientation inside the trimer. The linker representing a protein fold related to the prosegment of procarboxypeptidase A is in contact with only two of the three beta-subunits and directly interacts with the corresponding chromophores of these proteins. In addition to a modulation of the chromophores' spectral properties, the linker polypeptide attracts the alphabeta-subcomplexes, thereby bringing the beta-chromophores closer together. These results will enable interpretations of energy-transfer mechanisms within phycobiliproteins.

Organizational Affiliation

Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82158 Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 230.14 kDa
Atom Count: 17,502
Modeled Residue Count: 2,060
Deposited Residue Count: 2,060
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLOPHYCOCYANIN, ALPHA CHAIN	A, C, E, H, J A, C, E, H, J, L	160	Mastigocladus laminosus	Mutation(s): 0
UniProt
Find proteins for P00315 (Mastigocladus laminosus) Explore P00315 Go to UniProtKB: P00315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00315
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, D, F, I, K B, D, F, I, K, M	161	Mastigocladus laminosus	Mutation(s): 1
UniProt
Find proteins for P00318 (Mastigocladus laminosus) Explore P00318 Go to UniProtKB: P00318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00318
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE	G [auth N], N [auth O]	67	Mastigocladus laminosus	Mutation(s): 0
UniProt
Find proteins for P20116 (Mastigocladus laminosus) Explore P20116 Go to UniProtKB: P20116
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20116
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 Y [auth J] SDF format, chain X [auth I] SDF format, chain W [auth H] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain DA [auth M] SDF format, chain BA [auth L] SDF format, chain AA [auth K] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth I] MOL2 format, chain W [auth H] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain DA [auth M] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth K] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth I] mmCIF format, chain W [auth H] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain DA [auth M] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] DA [auth M] O [auth A] P [auth B] AA [auth K], BA [auth L], DA [auth M], O [auth A], P [auth B], Q [auth C], S [auth D], T [auth E], V [auth F], W [auth H], X [auth I], Y [auth J]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain DA [auth M] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J]
BO4 Query on BO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain U [auth E] SDF format, chain R [auth C] SDF format, chain CA [auth L] MOL2 format, chain Z [auth J] MOL2 format, chain U [auth E] MOL2 format, chain R [auth C] MOL2 format, chain CA [auth L] mmCIF format, chain Z [auth J] mmCIF format, chain U [auth E] mmCIF format, chain R [auth C] mmCIF format, chain CA [auth L]	CA [auth L], R [auth C], U [auth E], Z [auth J]	BORATE ION B H₄ O₄ KCFLOKKYWBPKFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth L] Focus chain R [auth C] Focus chain U [auth E] Focus chain Z [auth J]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256 (Depositor)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.12	α = 90
b = 151.9	β = 90
c = 137.85	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-02-23
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2022-12-21
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description
Version 2.0: 2025-02-26
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary