SAXSdb — 2w88

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

PLASTOCYANIN

PHORMIDIUM LAMINOSUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	COPPER (II) ION × 6 ZINC ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLAS_PHOLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–106； UniProt 35–139 Author chain B； PDBConstruct 2–106； UniProt 35–139 Author chain C； PDBConstruct 2–106； UniProt 35–139

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	2w88
Deposition date deposition_date	2009-01-14
Structure title title	Plastocyanin variant with N-terminal Methionine - open structure
Keywords keywords	PROTEIN INTERACTIONS, TRANSPORT, CUPREDOXIN, SELF-ASSEMBLY, METAL-BINDING, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

2w88__assembly_1__model_1

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

Download this curve (.dat)

2w88__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w88__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.30 Å
Rg (electron density)	27.35 Å
Total Rg	28.18 Å
Atom count	4898
Residues	636
Excluded volume	87207 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w88__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	PLASTOCYANIN
Molecular weight formula_weight	11563.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2449

METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG

Source Source

Source organism organism	PHORMIDIUM LAMINOSUM
NCBI taxonomy ID ncbi_taxonomy_id	32059
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2w88a_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2w88b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2w88c_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (3 domains)

Domain ID domain_id	2w88A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2w88B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2w88C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	127.700 Å
Unit-cell length b length_b	127.700 Å
Unit-cell length c length_c	94.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	110.430 Å
R factor r_factor	0.1958
R_work r_work	0.1943
R_free r_free	0.2228

Plastocyanin variant with N-terminal Methionine - open structure

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

PLASTOCYANIN

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

2w88__assembly_1__model_1

2w88__assembly_1__model_1 | I(q)

2w88__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Plastocyanin variant with N-terminal Methionine - open structure

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

PLASTOCYANIN

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

2w88__assembly_1__model_1

2w88__assembly_1__model_1 | I(q)

2w88__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)