1CPC | pdb_00001cpc

ISOLATION, CRYSTALLIZATION, CRYSTAL STRUCTURE ANALYSIS AND REFINEMENT OF CONSTITUTIVE C-PHYCOCYANIN FROM THE CHROMATICALLY ADAPTING CYANOBACTERIUM FREMYELLA DIPLOSIPHON AT 1.66 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1CPC/pdb

Classification: LIGHT HARVESTING PROTEIN
Organism(s): Microchaete diplosiphon
Mutation(s): No

Deposited: 1990-10-11 Released: 1993-01-15
Deposition Author(s): Duerring, M., Schmidt, G.B., Huber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Work:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Isolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium Fremyella diplosiphon at 1.66 A resolution.

Duerring, M., Schmidt, G.B., Huber, R.

(1991) J Mol Biology 217: 577-592

PubMed: 1899708 Search on PubMed
DOI: https://doi.org/10.1016/0022-2836(91)90759-y
Primary Citation Related Structures:
1CPC

PubMed Abstract:
Constitutive phycocyanin from cyanobacterium Fremyella diplosiphon (Calothrix sp. PCC 7601) grown in green light, has been isolated and crystallized. The crystals belong to the space group R3 with cell constants a = b = 180.26 A, c = 61.24 A, alpha = beta = 90 degrees, gamma = 120 degrees. The crystal structure has been determined by Patterson search techniques using the molecular model of C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum. The asymmetric unit of the crystal cell consists of two (alpha beta)-monomers related by a local dyad. Three asymmetric units are arranged around a crystallographic triad and form an (alpha beta)6-hexamer, the functional unit in the native antenna rod. The initial structure has been refined in a cyclic manner by energy-restrained crystallographic refinement and modelling until the conventional crystallographic R-factor converged at 18.1% with data to a resolution of 1.66 A. The molecular structure resembles closely the C-phycocyanins of Mastigocladus laminosus and A. quadruplicatum. The conformation and configuration of the alpha-84 and beta-84 chromophores is very similar to the corresponding chromophores in the trimeric C-phycocyanin of M. laminosus, whereas the beta-155 chromophore differs in configuration with C(4)-Z, C(10)-Z and C(15)-Z compared to C(4)-Z, C(10)-Z, C(15)-Z,E. The stereochemistry of the beta-155 chiral centres is C(2)-RC(3)-R and C(31)-S, respectively, whereas alpha-84 and beta-84 have C(2)-RC(3)-R and C(31)-R. The amino acid sequences of constitutive and inducible phycocyanin differ mainly in residues located on the surface of the beta-subunits that mediate the inter-hexameric contacts.

Organizational Affiliation

Max-Planck-Institut für Biochemie, München, Germany.

Macromolecule Content

Total Structure Weight: 73.92 kDa
Atom Count: 5,434
Modeled Residue Count: 668
Deposited Residue Count: 668
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, C [auth K]	162	Microchaete diplosiphon	Mutation(s): 0
UniProt
Find proteins for P07122 (Microchaete diplosiphon) Explore P07122 Go to UniProtKB: P07122
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07122
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, D [auth L]	172	Microchaete diplosiphon	Mutation(s): 0
UniProt
Find proteins for P07119 (Microchaete diplosiphon) Explore P07119 Go to UniProtKB: P07119
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07119
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 E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth K] SDF format, chain I [auth L] SDF format, chain J [auth L] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth K] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth K] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L]	E [auth A] F [auth B] G [auth B] H [auth K] I [auth L] E [auth A], F [auth B], G [auth B], H [auth K], I [auth L], J [auth L]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth K] Focus chain I [auth L] Focus chain J [auth L]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Work: 0.181 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.26	α = 90
b = 180.26	β = 90
c = 61.24	γ = 120

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1993-01-15

Deposition Author(s):

Duerring, M.

Schmidt, G.B.

Huber, R.

Revision History (Full details and data files)

Version 1.0: 1993-01-15
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-04-10
Changes: Non-polymer description, Structure summary
Version 1.4: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other