SAXSdb — 3g2c

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

Exodeoxyribonuclease

Methanothermobacter thermautotrophicus

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(PCPGPTPA)-3' × 1 GLYCEROL × 7 MAGNESIUM ION × 2 PHOSPHATE ION × 3 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O26314_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 1–257 Author chain B； PDBConstruct 1–257； UniProt 1–257

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	3g2c
Deposition date deposition_date	2009-01-31
Structure title title	Mth0212 in complex with a short ssDNA (CGTA)
Keywords keywords	protein-DNA complex, single-stranded DNA, flipped nucleotide, PO4, Mg2+, 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.

3g2c__assembly_1__model_1

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

Download this curve (.dat)

3g2c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g2c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.21 Å
Rg (electron density)	29.18 Å
Total Rg	29.74 Å
Atom count	4415
Residues	516
Excluded volume	77957 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g2c__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	Exodeoxyribonuclease
Molecular weight formula_weight	31430.7 kDa
EC 编号 ec_number	3.1.11.2
Mutation mutation	T2A
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	4586

MAVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIGLEIELLEHHHHHH

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	187420
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(PCPGPTPA)-3'
Molecular weight formula_weight	1190.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CGTA

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

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	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3g2ca1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.0 — automated matches

Domain ID domain_id	d3g2ca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3g2cb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3g2cA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	3g2cB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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Unit-cell length a length_a	80.325 Å
Unit-cell length b length_b	80.325 Å
Unit-cell length c length_c	79.611 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	28.270 Å
R factor r_factor	0.2070
R_work r_work	0.2040
R_free r_free	0.2630

Mth0212 in complex with a short ssDNA (CGTA)

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

Exodeoxyribonuclease

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

3g2c__assembly_1__model_1

3g2c__assembly_1__model_1 | I(q)

3g2c__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

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Mth0212 in complex with a short ssDNA (CGTA)

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

Exodeoxyribonuclease

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

3g2c__assembly_1__model_1

3g2c__assembly_1__model_1 | I(q)

3g2c__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

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (2)