SAXSdb — 1l8d

▼

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

DNA double-strand break repair rad50 ATPase

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 1 PHOSPHATE ION × 6 CITRIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD50_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–112； UniProt 396–506 Author chain B； PDBConstruct 2–112； UniProt 396–506

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1l8d
Deposition date deposition_date	2002-03-20
Structure title title	Rad50 coiled-coil Zn hook
Keywords keywords	zinc finger, rad50, DNA repair, Recombination, hook motif, REPLICATION; REPLICATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1l8d__assembly_1__model_1

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

Download this curve (.dat)

1l8d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l8d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.85 Å
Rg (electron density)	30.98 Å
Total Rg	31.06 Å
Atom count	1733
Residues	205
Excluded volume	30819 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l8d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA double-strand break repair rad50 ATPase
Molecular weight formula_weight	13153.3 kDa
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	1857

MKKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIKRLTPLLTVAE

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 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	124

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1l8da_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.12 — Rad50 coiled-coil Zn hook
Family Family family	h.4.12.1 — Rad50 coiled-coil Zn hook

Domain ID domain_id	d1l8db_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.12 — Rad50 coiled-coil Zn hook
Family Family family	h.4.12.1 — Rad50 coiled-coil Zn hook

CATH v4.4 (2 domains)

Domain ID domain_id	1l8dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	510 — Helix hairpin bin

Domain ID domain_id	1l8dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	510 — Helix hairpin bin

▶

Unit-cell length a length_a	31.958 Å
Unit-cell length b length_b	77.868 Å
Unit-cell length c length_c	53.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2780

Rad50 coiled-coil Zn hook

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

DNA double-strand break repair rad50 ATPase

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

1l8d__assembly_1__model_1

1l8d__assembly_1__model_1 | I(q)

1l8d__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 non-polymer

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 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Rad50 coiled-coil Zn hook

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

DNA double-strand break repair rad50 ATPase

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

1l8d__assembly_1__model_1

1l8d__assembly_1__model_1 | I(q)

1l8d__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 non-polymer

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 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)