SAXSdb — 2vf7

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

EXCINUCLEASE ABC, SUBUNIT A.

DEINOCOCCUS RADIODURANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 4 ZINC ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 4 ZINC ION × 4 MAGNESIUM ION × 2 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 2 ZINC ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 2 ZINC ION × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 2 ZINC ION × 2 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RYW8_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–842； UniProt 81–922 Author chain B； PDBConstruct 1–842； UniProt 81–922 Author chain C； PDBConstruct 1–842； UniProt 81–922

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	2vf7
Deposition date deposition_date	2007-10-31
Structure title title	Crystal structure of UvrA2 from Deinococcus radiodurans
Keywords keywords	;DNA-BINDING PROTEIN, NUCLEOTIDE-BINDING, ZINC-BINDING DOMAIN, SOS RESPONSE, METAL-BINDING, EXCISION NUCLEASE, ZINC-FINGER, ATP-BINDING, DNA-BINDING, DNA EXCISION, ZINC, CYTOPLASM, DNA DAMAGE, DNA REPAIR, ABC PROTEIN DNA-BINDING PROTEIN, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

2vf7__assembly_2__model_1

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

Download this curve (.dat)

2vf7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vf7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	38.63 Å
Rg (electron density)	37.92 Å
Total Rg	38.28 Å
Atom count	12598
Residues	1628
Excluded volume	222590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vf7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vf7__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vf7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2vf7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2vf7__assembly_5__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	EXCINUCLEASE ABC, SUBUNIT A.
Molecular weight formula_weight	91664.6 kDa
Mutation mutation	YES
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	19508

MTPSRPSPDFPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQPVNPDPEDDEDPADHTAGSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR

Source Source

Source organism organism	DEINOCOCCUS RADIODURANS
NCBI taxonomy ID ncbi_taxonomy_id	1299
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	597

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	2vf7A01
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	2vf7A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1580 — ABC transporter ATPase like fold
Homologous superfamily homologous superfamily	10 — ABC transporter ATPase like domain

Domain ID domain_id	2vf7A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	280 — ABC transporter ATPase domain-like

Domain ID domain_id	2vf7A04
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	2vf7B01
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	2vf7B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	280 — ABC transporter ATPase domain-like

Domain ID domain_id	2vf7B03
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	2vf7C01
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	2vf7C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1580 — ABC transporter ATPase like fold
Homologous superfamily homologous superfamily	10 — ABC transporter ATPase like domain

Domain ID domain_id	2vf7C03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	280 — ABC transporter ATPase domain-like

Domain ID domain_id	2vf7C04
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	271.710 Å
Unit-cell length b length_b	111.670 Å
Unit-cell length c length_c	103.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2230
R_work r_work	0.2190
R_free r_free	0.2950

Crystal structure of UvrA2 from Deinococcus radiodurans

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

EXCINUCLEASE ABC, SUBUNIT A.

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

2vf7__assembly_2__model_1

2vf7__assembly_2__model_1 | I(q)

2vf7__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 (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) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Crystal structure of UvrA2 from Deinococcus radiodurans

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

EXCINUCLEASE ABC, SUBUNIT A.

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

2vf7__assembly_2__model_1

2vf7__assembly_2__model_1 | I(q)

2vf7__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 (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) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)