SAXSdb — 2q48

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

Protein At5g48480

Arabidopsis thaliana

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y5848_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 1–166 Author chain B； PDBConstruct 1–166； UniProt 1–166

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	2q48
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g48480
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT5G48480, REDUCTIVELY METHYLATED PROTEIN, CATH 3.10.180 FOLD, UNKNOWN FUNCTION, DIMER, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG ;; 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.

2q48__assembly_1__model_2

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

Download this curve (.dat)

2q48__assembly_1__model_2 | I(q)

100 plotted points; both axes use logarithmic scales.

2q48__assembly_1__model_2 | P(r) · Pending

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

Rg（Guinier）	18.46 Å
Rg (electron density)	17.27 Å
Total Rg	18.27 Å
Atom count	1782
Residues	240
Excluded volume	32063 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q48__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q48__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q48__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q48__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q48__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q48__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q48__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q48__assembly_1__model_8`	dimeric （2）	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)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q48a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.9 — Hypothetical protein At5g48480

Domain ID domain_id	d2q48b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.9 — Hypothetical protein At5g48480

CATH v4.4 (2 domains)

Domain ID domain_id	2q48A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	2q48B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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Unit-cell length a length_a	55.871 Å
Unit-cell length b length_b	55.871 Å
Unit-cell length c length_c	147.341 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	27.447 Å
R factor r_factor	0.1670
R_work r_work	0.1670
R_free r_free	0.2140

Description description	Protein At5g48480
Molecular weight formula_weight	17668.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	16272

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g48480

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

Protein At5g48480

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

2q48__assembly_1__model_2

2q48__assembly_1__model_2 | I(q)

2q48__assembly_1__model_2 | 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	252

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g48480

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

Protein At5g48480

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

2q48__assembly_1__model_2

2q48__assembly_1__model_2 | I(q)

2q48__assembly_1__model_2 | 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)