SAXSdb — 6p66

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

DNA repair protein RAD25

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA endonuclease Bax1 × 1 （O29890） CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA endonuclease Bax1 × 1 （O29890） CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O29889_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–471； UniProt 1–452 Author chain C； PDBConstruct 20–471； UniProt 1–452

DNA endonuclease Bax1

Archaeoglobus fulgidus DSM 4304

UniProt O29890

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 RAD25 × 1 （O29889） CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA repair protein RAD25 × 1 （O29889） CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O29890_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–468； UniProt 1–468 Author chain D； PDBConstruct 1–468； UniProt 1–468

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	6p66
Deposition date deposition_date	2019-06-03
Structure title title	The crystal structure of the XPB complex with Bax1 from Archaeoglobus fulgidus at 3.0 Angstrom resolution
Keywords keywords	Helicase, nuclease, complex, 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.

6p66__assembly_2__model_1

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

Download this curve (.dat)

6p66__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p66__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.74 Å
Rg (electron density)	37.74 Å
Total Rg	37.87 Å
Atom count	6752
Residues	927
Excluded volume	118790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p66__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6p66__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA repair protein RAD25
Molecular weight formula_weight	53885.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	13249

MGSSHHHHHSSGLVPRGSHMQMIAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTGEVNTARRRKNAAKGAA

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA endonuclease Bax1
Molecular weight formula_weight	54808.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MLPKELLDVRRAKGRIFPKFADERDYELAEKVIEIFKKGLGKKYGNLMKQARKLENAKNFKKVRGFIRVLENHCIEKSCAFDVDSELEPRKVRMLLFEHGFVTSKKERDRVLEYVARYFSTTPETVERAMYADREEELILTKFRPLTPDNLIKLYNLSLLQTTLFNALRLTFWASDRHKEIFRSIKRLGLMYELYEDSGRLMVEVTGAATLLKMTRKYGVSFAKLIPWILRAKNWFIRAEISDFDRLYIMEIDDRIRDLFPDVEERLSYDSTLEEEFARKMQMLGYEVEREPDVVKAGKYAFIPDFAVNLGDKKVYIEIAGFWTDEYLRKKAEKIKSSSIPLILIAREDFGDGGANVKDVILFSRKIPYGEVIKALKRYKPEKKVEGDVVELENFAEVPSEYVIAGKYAVRREIFEEIKREIEVSNPSTLEDIKAILKKYGLGESAIRAFGYRVRWIGLGEAVIERTD

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6p66a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d6p66a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

CATH v4.4 (3 domains)

Domain ID domain_id	6p66B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6p66C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6p66D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	200.600 Å
Unit-cell length b length_b	129.840 Å
Unit-cell length c length_c	108.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	39.932 Å
R factor r_factor	0.2266
R_work r_work	0.2251
R_free r_free	0.2399

The crystal structure of the XPB complex with Bax1 from Archaeoglobus fulgidus at 3.0 Angstrom resolution

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

DNA repair protein RAD25

State in the Current Structure

Other States of the Same Protein in the Database

DNA endonuclease Bax1

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

6p66__assembly_2__model_1

6p66__assembly_2__model_1 | I(q)

6p66__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The crystal structure of the XPB complex with Bax1 from Archaeoglobus fulgidus at 3.0 Angstrom resolution

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

DNA repair protein RAD25

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 endonuclease Bax1

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

6p66__assembly_2__model_1

6p66__assembly_2__model_1 | I(q)

6p66__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)