SAXSdb — 3gpl

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

Exodeoxyribonuclease V, subunit RecD, putative

Deinococcus radiodurans R1

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(TTPTPTPTPTPTPT)-3' × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(TTPTPTPTPTPTPT)-3' × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RT63_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–566； UniProt 151–715 Author chain B； PDBConstruct 2–566； UniProt 151–715

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	3gpl
Deposition date deposition_date	2009-03-23
Structure title title	Crystal structure of the ternary complex of RecD2 with DNA and ADPNP
Keywords keywords	ALPHA AND BETA PROTEIN, ATP-BINDING, NUCLEOTIDE-BINDING, HELICASE, 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.

3gpl__assembly_2__model_1

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

Download this curve (.dat)

3gpl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gpl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.21 Å
Rg (electron density)	24.44 Å
Total Rg	25.15 Å
Atom count	4056
Residues	523
Excluded volume	71654 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gpl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gpl__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 (5)

Entity 1 Entity 1 polymer

Description description	Exodeoxyribonuclease V, subunit RecD, putative
Molecular weight formula_weight	61465.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8322

MSQQGLERRLLAGLQGLGLTINQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSEDDSPLFAAEAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRAHLEHHHHHH

Source Source

Source organism organism	Deinococcus radiodurans R1
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(TTPTPTPTPTPTPT)-3'
Molecular weight formula_weight	2388.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X,Y

TTTTTTTT

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	186

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	3gplA02
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	3gplA03
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	3gplA04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	940 —

Domain ID domain_id	3gplB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2220 —

Domain ID domain_id	3gplB02
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	3gplB03
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	3gplB04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	940 —

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Unit-cell length a length_a	66.120 Å
Unit-cell length b length_b	130.360 Å
Unit-cell length c length_c	80.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	43.270 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2730

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

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

Exodeoxyribonuclease V, subunit RecD, putative

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

3gpl__assembly_2__model_1

3gpl__assembly_2__model_1 | I(q)

3gpl__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (2)

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

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

Exodeoxyribonuclease V, subunit RecD, putative

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

3gpl__assembly_2__model_1

3gpl__assembly_2__model_1 | I(q)

3gpl__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (2)