SAXSdb — 2q4j

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

Probable UTP-glucose-1-phosphate uridylyltransferase 2

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UGPA2_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–469； UniProt 1–469 Author chain B； PDBConstruct 1–469； UniProt 1–469

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	2q4j
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT3G03250, PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, TRANSFERASE ;; TRANSFERASE
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.

2q4j__assembly_2__model_7

Assembly 2 · Model 7 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q4j__assembly_2__model_7 | I(q)

100 plotted points; both axes use logarithmic scales.

2q4j__assembly_2__model_7 | P(r) · Pending

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

Rg（Guinier）	24.47 Å
Rg (electron density)	23.30 Å
Total Rg	24.21 Å
Atom count	3543
Residues	455
Excluded volume	63880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q4j__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q4j__assembly_1__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q4j__assembly_1__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q4j__assembly_1__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q4j__assembly_1__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q4j__assembly_1__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q4j__assembly_1__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q4j__assembly_1__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q4j__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2q4j__assembly_2__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	3	`2q4j__assembly_2__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	4	`2q4j__assembly_2__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	5	`2q4j__assembly_2__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	6	`2q4j__assembly_2__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	7	`2q4j__assembly_2__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	8	`2q4j__assembly_2__model_8`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Probable UTP-glucose-1-phosphate uridylyltransferase 2
Molecular weight formula_weight	51798.2 kDa
EC 编号 ec_number	2.7.7.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	60344

MAATTENLPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	421

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2q4ja1
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.4 — GlmU C-terminal domain-like

Domain ID domain_id	d2q4ja2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.5 — UDP-glucose pyrophosphorylase

Domain ID domain_id	d2q4jb1
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.4 — GlmU C-terminal domain-like

Domain ID domain_id	d2q4jb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.5 — UDP-glucose pyrophosphorylase

CATH v4.4 (4 domains)

Domain ID domain_id	2q4jA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2q4jA02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	2q4jB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2q4jB02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	188.680 Å
Unit-cell length b length_b	58.863 Å
Unit-cell length c length_c	89.862 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.863 Å
Low-resolution limit resolution_low	37.365 Å
R factor r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.2310

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase

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

Probable UTP-glucose-1-phosphate uridylyltransferase 2

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

2q4j__assembly_2__model_7

2q4j__assembly_2__model_7 | I(q)

2q4j__assembly_2__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase

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

Probable UTP-glucose-1-phosphate uridylyltransferase 2

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

2q4j__assembly_2__model_7

2q4j__assembly_2__model_7 | I(q)

2q4j__assembly_2__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)