SAXSdb — 2nmv

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

UvrABC system protein B

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 1	5'-D(PTPTPTPTP*T)-3' × 1 N-METHYLACETAMIDE × 1 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UVRB_BACSU
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–661； UniProt 1–661 Author chain B； PDBConstruct 1–38； UniProt 622–659

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	2nmv
Deposition date deposition_date	2006-10-23
Structure title title	Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA
Keywords keywords	Protein-DNA complex, T-fluorescein, hairpin, 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.

2nmv__assembly_1__model_1

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

Download this curve (.dat)

2nmv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nmv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.08 Å
Rg (electron density)	28.18 Å
Total Rg	28.92 Å
Atom count	5311
Residues	663
Excluded volume	93842 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nmv__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	5'-D(PTPTPTPTP*T)-3'
Molecular weight formula_weight	1476.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	5311

TTTTT

Entity 2 Entity 2 polymer

Description description	UvrABC system protein B
Molecular weight formula_weight	76440.1 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKDRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINKEIRDVIRATVAAEDKAEYKTKAAPKLSKMTKKERQKVVEQMEHEMKEAAKALDFERAAELRDLLLELKAEG

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	UvrABC system protein B
Molecular weight formula_weight	4506.2 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KERQKVVEQMEHEMKEAAKALDFERAAELRDLLLELKA

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	N-METHYLACETAMIDE
Molecular weight formula_weight	73.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
Molecular weight formula_weight	332.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2nmvA01
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	2nmvA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2060 — Penicillin-binding protein 1b fold
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 1b domain

Domain ID domain_id	2nmvA04
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	74.410 Å
Unit-cell length b length_b	95.597 Å
Unit-cell length c length_c	97.878 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	68.360 Å
R factor r_factor	0.2271
R_work r_work	0.2243
R_free r_free	0.2807

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted 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

2nmv__assembly_1__model_1

2nmv__assembly_1__model_1 | I(q)

2nmv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted 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

2nmv__assembly_1__model_1

2nmv__assembly_1__model_1 | I(q)

2nmv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)