SAXSdb — 2av4

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

Thioredoxin-like protein 4A (DIM1)

Plasmodium yoelii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 4 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 24 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7R866_PLAYO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–160； UniProt 2–142

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	2av4
Deposition date deposition_date	2005-08-29
Structure title title	Crystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1)
Keywords keywords	;thioredoxin-like protein, DIM1, U5 snRNP-specific 15kD protein, Structural Genomics, Structural Genomics Consortium, SGC, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2av4__assembly_1__model_1

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

Download this curve (.dat)

2av4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2av4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.42 Å
Rg (electron density)	13.87 Å
Total Rg	15.14 Å
Atom count	1119
Residues	135
Excluded volume	19915 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2av4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2av4__assembly_2__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	Thioredoxin-like protein 4A (DIM1)
Molecular weight formula_weight	18696.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1318

MGSSHHHHHHSSGLVPRGSSFMLQHLNSGWAVDQAIVNEDERLVCIRFGHDYDPDCMKMDELLYKVADDIKNFCVIYLVDITEVPDFNTMYELYDPVSVMFFYRNKHMMIDLGTGNNNKINWPMNNKQEFIDIVETIFRGARKGRGLVISPKDYSTKYKY

Source Source

Source organism organism	Plasmodium yoelii
NCBI taxonomy ID ncbi_taxonomy_id	5861
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2av4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d2av4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2av4A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	109.877 Å
Unit-cell length b length_b	109.877 Å
Unit-cell length c length_c	85.170 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	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	41.500 Å
R factor r_factor	0.2096
R_work r_work	0.2080
R_free r_free	0.2611

Crystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1)

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

Thioredoxin-like protein 4A (DIM1)

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

2av4__assembly_1__model_1

2av4__assembly_1__model_1 | I(q)

2av4__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1)

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

Thioredoxin-like protein 4A (DIM1)

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

2av4__assembly_1__model_1

2av4__assembly_1__model_1 | I(q)

2av4__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)