SAXSdb — 3dw9

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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(DGPDAPDGPDTPDCPDCPDAPDCPDCPDGPDGPDTPDGPDGPDAPDCPDTPDC)-3') ; × 2 MANGANESE (II) ION × 4 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	2
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	3dw9
Deposition date deposition_date	2008-07-21
Structure title title	SgrAI with cognate DNA and manganese bound
Keywords keywords	restriction enzyme-DNA complex, 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.

3dw9__assembly_1__model_1

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

Download this curve (.dat)

3dw9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dw9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.80 Å
Rg (electron density)	27.10 Å
Total Rg	27.73 Å
Atom count	6008
Residues	705
Excluded volume	104200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dw9__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 (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DGPDAPDGPDTPDCPDCPDAPDCPDCPDGPDGPDTPDGPDGPDAPDCPDTPDC)-3') ;
Molecular weight formula_weight	5517.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F
Atom count atom_count	6335

GAGTCCACCGGTGGACTC

Entity 2 Entity 2 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

PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3dw9A00
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	3dw9B00
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	58.261 Å
Unit-cell length b length_b	117.101 Å
Unit-cell length c length_c	63.702 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.96 °
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	2.200 Å
Low-resolution limit resolution_low	58.620 Å
R factor r_factor	0.1768
R_work r_work	0.1735
R_free r_free	0.2396

SgrAI with cognate DNA and manganese bound

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

3dw9__assembly_1__model_1

3dw9__assembly_1__model_1 | I(q)

3dw9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

SgrAI with cognate DNA and manganese bound

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

3dw9__assembly_1__model_1

3dw9__assembly_1__model_1 | I(q)

3dw9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)