4ALO | pdb_00004alo

STRUCTURE AND PROPERTIES OF H1 CRUSTACYANIN FROM LOBSTER HOMARUS AMERICANUS

PDB DOI: https://doi.org/10.2210/pdb4ALO/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homarus americanus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-03-05 Released: 2012-08-08
Deposition Author(s): Ferrari, M., Folli, C., Pincolini, E., Mcclintock, T.S., Roessle, M., Berni, R., Cianci, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.266 (Depositor), 0.266 (DCC)
R-Value Work:
0.222 (Depositor), 0.221 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural Characterization of Recombinant Crustacyanin Subunits from the Lobster Homarus Americanus.

Ferrari, M., Folli, C., Pincolini, E., Mcclintock, T.S., Rossle, M., Berni, R., Cianci, M.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 846

PubMed: 22869108 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309112026103
Primary Citation Related Structures:
4ALO

PubMed Abstract:
Crustacean crustacyanin proteins are linked to the production and modification of carapace colour, with direct implications for fitness and survival. Here, the structural and functional properties of the two recombinant crustacyanin subunits H(1) and H(2) from the American lobster Homarus americanus are reported. The two subunits are structurally highly similar to the corresponding natural apo crustacyanin CRTC and CRTA subunits from the European lobster H. gammarus. Reconstitution studies of the recombinant crustacyanin proteins H(1) and H(2) with astaxanthin reproduced the bathochromic shift of 85-95 nm typical of the natural crustacyanin subunits from H. gammarus in complex with astaxanthin. Moreover, correlations between the presence of crustacyanin genes in crustacean species and the resulting carapace colours with the spectral properties of the subunits in complex with astaxanthin confirmed this genotype-phenotype linkage.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.

Macromolecule Content

Total Structure Weight: 42.53 kDa
Atom Count: 3,084
Modeled Residue Count: 362
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H1 APOCRUSTACYANIN	A, B	181	Homarus americanus	Mutation(s): 0
UniProt
Find proteins for P80029 (Homarus gammarus) Explore P80029 Go to UniProtKB: P80029
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80029
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth A], I [auth B], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.266 (Depositor), 0.266 (DCC)
R-Value Work: 0.222 (Depositor), 0.221 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.368	α = 90
b = 78.423	β = 90
c = 105.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2012-08-15
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

4ALO | pdb_00004alo

STRUCTURE AND PROPERTIES OF H1 CRUSTACYANIN FROM LOBSTER HOMARUS AMERICANUS

Literature

Structural Characterization of Recombinant Crustacyanin Subunits from the Lobster Homarus Americanus.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand