SAXSdb — 3lqc

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

DNA repair protein XRCC1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase beta × 1 （P06766） SODIUM ION × 1 CARBONATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 1–183

DNA polymerase beta

Rattus norvegicus

UniProt P06766

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA repair protein XRCC1 × 1 （P18887） SODIUM ION × 1 CARBONATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOLB_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 142–335

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	3lqc
Deposition date deposition_date	2010-02-09
Structure title title	X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain
Keywords keywords	;ALLOSTERIC DISULFIDE, SCAFFOLDING PROTEIN, DNA REPAIR, DNA DAMAGE, Nucleus, Phosphoprotein, Polymorphism, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Lyase, Magnesium, Metal-binding, Nucleotidyltransferase, Sodium, Transferase, DNA-BINDING PROTEIN, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

3lqc__assembly_1__model_1

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

Download this curve (.dat)

3lqc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lqc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.02 Å
Rg (electron density)	25.32 Å
Total Rg	25.97 Å
Atom count	2726
Residues	345
Excluded volume	48112 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lqc__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 (5)

Entity 1 Entity 1 polymer

Description description	DNA repair protein XRCC1
Molecular weight formula_weight	21060.5 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	2972

MPEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHSVDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDRVKIVCSQPYSKDSPFGLSFVRFHSPPDKDEAEAPSQKVTVTKLGQFRVKEEDESANHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase beta
Molecular weight formula_weight	23523.5 kDa
EC 编号 ec_number	2.7.7.7, 4.2.99.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSEHHHHHH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3lqca_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.8 — N-terminal domain of xrcc1

CATH v4.4 (3 domains)

Domain ID domain_id	3lqcA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3lqcB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	3lqcB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

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Unit-cell length a length_a	75.240 Å
Unit-cell length b length_b	75.240 Å
Unit-cell length c length_c	126.160 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.349 Å
Low-resolution limit resolution_low	24.628 Å
R factor r_factor	0.1920
R_work r_work	0.1890
R_free r_free	0.2500

X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain

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

DNA repair protein XRCC1

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase beta

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

3lqc__assembly_1__model_1

3lqc__assembly_1__model_1 | I(q)

3lqc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain

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

DNA repair protein XRCC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase beta

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

3lqc__assembly_1__model_1

3lqc__assembly_1__model_1 | I(q)

3lqc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)