SAXSdb — 1rxv

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

Flap structure-specific endonuclease

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-d(TpApGpCpApTpCpG*pG) × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	5'-d(TpApGpCpApTpCpG*pG) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FEN_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 1–336 Author chain B； PDBConstruct 1–336； UniProt 1–336

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	1rxv
Deposition date deposition_date	2003-12-18
Structure title title	Crystal Structure of A. Fulgidus FEN-1 bound to DNA
Keywords keywords	;helical clamp, helix-3 turn-helix, 3' flap binding site, protein-dna complex, dna repair, dna replication, HYDROLASE-DNA COMPLEX ;; HYDROLASE/DNA
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.

1rxv__assembly_2__model_1

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

Download this curve (.dat)

1rxv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rxv__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.86 Å
Rg (electron density)	20.85 Å
Total Rg	21.79 Å
Atom count	2484
Residues	307
Excluded volume	44219 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rxv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rxv__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Description description	5'-d(TpApGpCpApTpCpG*pG)
Molecular weight formula_weight	2755.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4968

TAGCATCGG

Entity 2 Entity 2 polymer

Description description	Flap structure-specific endonuclease
Molecular weight formula_weight	38117.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MGADIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNFFLNPPVTDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKSTQATLERWF

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rxva1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family family	a.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	d1rxva2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.120 — PIN domain-like
Superfamily Superfamily superfamily	c.120.1 — PIN domain-like
Family Family family	c.120.1.2 — 5' to 3' exonuclease catalytic domain

Domain ID domain_id	d1rxvb1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.7 — 5' to 3' exonuclease, C-terminal subdomain
Family Family family	a.60.7.1 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	d1rxvb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.120 — PIN domain-like
Superfamily Superfamily superfamily	c.120.1 — PIN domain-like
Family Family family	c.120.1.2 — 5' to 3' exonuclease catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1rxvA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

Domain ID domain_id	1rxvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1rxvB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

Domain ID domain_id	1rxvB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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Unit-cell length a length_a	86.843 Å
Unit-cell length b length_b	86.843 Å
Unit-cell length c length_c	250.519 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2760
R_work r_work	0.2740
R_free r_free	0.3090

Crystal Structure of A. Fulgidus FEN-1 bound to DNA

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

Flap structure-specific endonuclease

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

1rxv__assembly_2__model_1

1rxv__assembly_2__model_1 | I(q)

1rxv__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of A. Fulgidus FEN-1 bound to DNA

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

Flap structure-specific endonuclease

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

1rxv__assembly_2__model_1

1rxv__assembly_2__model_1 | I(q)

1rxv__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)