SAXSdb — 6o8g

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

UvrABC system protein B

Bacillus caldotenax

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(TPCPTPCPCPAPTPCPGPCPGPCPTPAPC)-3') ; × 1 ;DNA (5'-D(GPGPTPAPGPCPGPCPGPAPTPGPGPAPGP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 1 SODIUM ION × 1 water × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(TPCPTPCPCPAPTPCPGPCPGPCPTPAPC)-3') ; × 1 ;DNA (5'-D(GPGPTPAPGPCPGPCPGPAPTPGPGPAPGP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 1 CHLORIDE ION × 1 water × 1	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(TPCPTPCPCPAPTPCPGPCPGPCPTPAPC)-3') ; × 1 ;DNA (5'-D(GPGPTPAPGPCPGPCPGPAPTPGPGPAPGP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UVRB_BACCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–593； UniProt 2–593 Author chain B； PDBConstruct 1–593； UniProt 2–593 Author chain C； PDBConstruct 1–593； UniProt 2–593

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	6o8g
Deposition date deposition_date	2019-03-10
Structure title title	Crystal structure of UvrB bound to fully duplex DNA
Keywords keywords	DNA repair, nucleotide excision repair, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

6o8g__assembly_2__model_1

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

Download this curve (.dat)

6o8g__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o8g__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.10 Å
Rg (electron density)	27.45 Å
Total Rg	28.16 Å
Atom count	5224
Residues	598
Excluded volume	90794 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o8g__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6o8g__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6o8g__assembly_3__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	UvrABC system protein B
Molecular weight formula_weight	68157.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	15645

VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVCYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSSIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHSIRVEFFGDEIERIREVDALTGEVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFSSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIR

Source Source

Source organism organism	Bacillus caldotenax
NCBI taxonomy ID ncbi_taxonomy_id	1395
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPTPCPCPAPTPCPGPCPGPCPTPAP*C)-3') ;
Molecular weight formula_weight	4480.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F,H

TCTCCATCGCGCTAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPGPTPAPGPCPGPCPGPAPTPGPGPAPGPA)-3') ;
Molecular weight formula_weight	5028.3 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,I

GGTAGCGCGATGGAGA

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6o8gA01
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	6o8gC01
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

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Unit-cell length a length_a	170.685 Å
Unit-cell length b length_b	201.181 Å
Unit-cell length c length_c	62.664 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.640 Å
Low-resolution limit resolution_low	48.240 Å
R factor r_factor	0.2228
R_work r_work	0.2200
R_free r_free	0.2738

Crystal structure of UvrB bound to fully duplex DNA

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

UvrABC system protein B

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

6o8g__assembly_2__model_1

6o8g__assembly_2__model_1 | I(q)

6o8g__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of UvrB bound to fully duplex DNA

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

UvrABC system protein B

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

6o8g__assembly_2__model_1

6o8g__assembly_2__model_1 | I(q)

6o8g__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)