SAXSdb — 3bm3

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

PspGI restriction endonuclease

Pyrococcus sp. GI-H

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(CPAPTPCPCPAPGPGPTPAPC)-3') ; × 1 ;DNA (5'-D(GPGPTPAPCPCPTPGPGPAPT)-3') ; × 1 CITRIC ACID × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O93646_9EURY
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–272； UniProt 1–272 Author chain B； PDBConstruct 1–272； UniProt 1–272

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	3bm3
Deposition date deposition_date	2007-12-12
Structure title title	Restriction endonuclease PspGI-substrate DNA complex
Keywords keywords	ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, PSPGI, BASE FLIPPING, 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.

3bm3__assembly_1__model_1

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

Download this curve (.dat)

3bm3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bm3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.84 Å
Rg (electron density)	24.15 Å
Total Rg	24.95 Å
Atom count	4777
Residues	535
Excluded volume	83928 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bm3__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	;DNA (5'-D(CPAPTPCPCPAPGPGPTPAP*C)-3') ;
Molecular weight formula_weight	3318.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	5301

CATCCAGGTAC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPGPTPAPCPCPTPGPGPAP*T)-3') ;
Molecular weight formula_weight	3389.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GGTACCTGGAT

Entity 3 Entity 3 polymer

Description description	PspGI restriction endonuclease
Molecular weight formula_weight	32215.3 kDa
Mutation mutation	D138A, A146T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MVRNLVIDITKKPTQNIPPTNEIIEEAITELNVDELLDRLFEKDESGEVITPSRIAKMLEEKAFEIYKEYEKQVREAYLSAGYSREKLEQSFQQARFSRGGKAFEIIFTKLLNKFGIRYEHDRVIKIYDYITEGEKPAFIIPSVRTFLNDPSSAILITVKRKVRERWREAVGEAQILRNKFGDEINFWFVGFDEEFTIYSAIAMLDNGIDRVYVIDGRYDSLIEEIKRISDPNFNEDKYIQKIRRFSDIFDDIIQFLNKHGNKKRGKQLTLV

Source Source

Source organism organism	Pyrococcus sp. GI-H
NCBI taxonomy ID ncbi_taxonomy_id	83521
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 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	293

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3bm3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	3bm3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	80 —

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Unit-cell length a length_a	46.884 Å
Unit-cell length b length_b	96.060 Å
Unit-cell length c length_c	127.069 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.380 Å
R factor r_factor	0.1710
R_work r_work	0.1698
R_free r_free	0.1924

Restriction endonuclease PspGI-substrate DNA complex

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

PspGI restriction endonuclease

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

3bm3__assembly_1__model_1

3bm3__assembly_1__model_1 | I(q)

3bm3__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 (5)

Restriction endonuclease PspGI-substrate DNA complex

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

PspGI restriction endonuclease

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

3bm3__assembly_1__model_1

3bm3__assembly_1__model_1 | I(q)

3bm3__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 (5)