SAXSdb — 3n7b

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

SgraIR restriction enzyme

Streptomyces griseus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(APGPTPCPCPAPCPCPGPGPGPGPGPAPCPT)-3') ; × 1 ;DNA (5'-D(APGPTPCPCPCPCPCPGPGPTPGPGPAPCPT)-3') ; × 1 CALCIUM ION × 3 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9F6L0_STRGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 2–339 Author chain B； PDBConstruct 1–338； UniProt 2–339

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	3n7b
Deposition date deposition_date	2010-05-26
Structure title title	SgrAI bound to secondary site DNA and Ca(II)
Keywords keywords	restriction endonuclease, 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.

3n7b__assembly_1__model_1

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

Download this curve (.dat)

3n7b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3n7b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.93 Å
Rg (electron density)	27.26 Å
Total Rg	27.90 Å
Atom count	5917
Residues	701
Excluded volume	102880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3n7b__assembly_1__model_1`	tetrameric （4）	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	SgraIR restriction enzyme
Molecular weight formula_weight	37941.9 kDa
EC 编号 ec_number	3.1.21.4
Mutation mutation	N63D
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	6970

PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG

Source Source

Source organism organism	Streptomyces griseus
NCBI taxonomy ID ncbi_taxonomy_id	1911
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APGPTPCPCPAPCPCPGPGPGPGPGPAPCPT)-3') ;
Molecular weight formula_weight	4924.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AGTCCACCGGGGGACT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APGPTPCPCPCPCPCPGPGPTPGPGPAPCPT)-3') ;
Molecular weight formula_weight	4875.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AGTCCCCCGGTGGACT

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	395

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3n7bA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3n7bB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	108.682 Å
Unit-cell length b length_b	133.662 Å
Unit-cell length c length_c	64.748 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	8

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

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	84.320 Å
R factor r_factor	0.1762
R_work r_work	0.1726
R_free r_free	0.2478

SgrAI bound to secondary site DNA and Ca(II)

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

SgraIR restriction enzyme

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

3n7b__assembly_1__model_1

3n7b__assembly_1__model_1 | I(q)

3n7b__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

SgrAI bound to secondary site DNA and Ca(II)

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

SgraIR restriction enzyme

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

3n7b__assembly_1__model_1

3n7b__assembly_1__model_1 | I(q)

3n7b__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)