SAXSdb — 8ov5

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Peridinin-chlorophyll a-binding protein 1, chloroplastic

Amphidinium carterae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	CHLOROPHYLL A × 6 PERIDININ × 24 ;[(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (5~{Z},8~{Z},11~{Z},14~{Z},17~{Z})-icosa-5,8,11,14,17-pentaenoate ; × 6 TETRAETHYLENE GLYCOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCP1_AMPCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain M； PDBConstruct 1–312； UniProt 58–369 Author chain N； PDBConstruct 1–312； UniProt 58–369 Author chain O； PDBConstruct 1–312； UniProt 58–369

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ov5
Deposition date deposition_date	2023-04-25
Structure title title	PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K
Keywords keywords	Light Harvesting, Carotenoid, Chlorophyll, Lipid, Dinoflagellates, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8ov5__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8ov5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ov5__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.98 Å
Rg (electron density)	33.34 Å
Total Rg	34.07 Å
Atom count	17793
Residues	936
Excluded volume	162600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ov5__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Peridinin-chlorophyll a-binding protein 1, chloroplastic
Molecular weight formula_weight	32521.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O
Atom count atom_count	20859

DEIGDAAKKLGDASYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVMGAAADPKLLKAAAEAHHKAIGSVSGPNGVTSRADWDNVNAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVNGADAEKAYEGFLAFKDVVKKSQVTSAAGPATVPSGDKIGVAAQQLSEASYPFLKEIDWLSDVYMKPLPGVSAQQSLKAIDKMIVMGAQADGNALKAAAEAHHKAIGSIDATGVTSAADYAAVNAALGRVIASVPKSTVMDVYNAMAGVTDTSIPLNMFSKVNPLDANAAAKAFYTFKDVVQAAQ

Source Source

Source organism organism	Amphidinium carterae
NCBI taxonomy ID ncbi_taxonomy_id	2961
Host organism host_organism	Amphidinium carterae

Entity 2 Entity 2 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PERIDININ
Molecular weight formula_weight	630.8 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 4 Entity 4 non-polymer

Description description	;[(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (5~{Z},8~{Z},11~{Z},14~{Z},17~{Z})-icosa-5,8,11,14,17-pentaenoate ;
Molecular weight formula_weight	959.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1792

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Unit-cell length a length_a	197.140 Å
Unit-cell length b length_b	115.610 Å
Unit-cell length c length_c	65.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.150 Å
Low-resolution limit resolution_low	43.380 Å
R factor r_factor	0.1414
R_work r_work	0.1407
R_free r_free	0.1547

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peridinin-chlorophyll a-binding protein 1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ov5__assembly_1__model_1

8ov5__assembly_1__model_1 | I(q)

8ov5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peridinin-chlorophyll a-binding protein 1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ov5__assembly_1__model_1

8ov5__assembly_1__model_1 | I(q)

8ov5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)