SAXSdb — 3ufm

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

Uracil-DNA glycosylase

Deinococcus radiodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Single-stranded DNA-binding protein × 1 （Q9RY51） IODIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 1–247

Single-stranded DNA-binding protein

OrganismNot specified

UniProt Q9RY51

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Uracil-DNA glycosylase × 1 （Q9RWH9） IODIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSB_DEIRA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 290–301

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	3ufm
Deposition date deposition_date	2011-11-01
Structure title title	Co-crystal structure of Deinococcus radiodurans uracil-DNA glycosylase and the C-terminus of the single-stranded DNA-binding protein
Keywords keywords	Glycosylase, SSB C-terminal, Base excision repair, hydrolase; HYDROLASE
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.

3ufm__assembly_1__model_1

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

Download this curve (.dat)

3ufm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ufm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.53 Å
Rg (electron density)	17.17 Å
Total Rg	18.29 Å
Atom count	1876
Residues	234
Excluded volume	33492 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ufm__assembly_1__model_1`	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 (4)

Entity 1 Entity 1 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	28851.6 kDa
EC 编号 ec_number	3.2.2.27
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	2029

MTDQPDLFGLAPDAPRPIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATVTEELEHHHHHH

Source Source

Source organism organism	Deinococcus radiodurans
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Single-stranded DNA-binding protein
Molecular weight formula_weight	1435.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DDFPPEEDDLPF

Entity 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3ufmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	470 — Uracil-DNA Glycosylase, subunit E
Homologous superfamily homologous superfamily	10 — Uracil-DNA glycosylase-like domain

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Unit-cell length a length_a	78.343 Å
Unit-cell length b length_b	92.640 Å
Unit-cell length c length_c	66.012 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1720
R_work r_work	0.1700
R_free r_free	0.2081

Co-crystal structure of Deinococcus radiodurans uracil-DNA glycosylase and the C-terminus of the single-stranded DNA-binding protein

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

Uracil-DNA glycosylase

State in the Current Structure

Other States of the Same Protein in the Database

Single-stranded DNA-binding protein

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

3ufm__assembly_1__model_1

3ufm__assembly_1__model_1 | I(q)

3ufm__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Co-crystal structure of Deinococcus radiodurans uracil-DNA glycosylase and the C-terminus of the single-stranded DNA-binding protein

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

Uracil-DNA glycosylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Single-stranded DNA-binding protein

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

3ufm__assembly_1__model_1

3ufm__assembly_1__model_1 | I(q)

3ufm__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)