SAXSdb — 5hlt

▼

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

Restriction endonuclease R.BpuJI

Bacillus pumilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPYPYTPAPCPCPCPGPTPGPGPA)-3') ; × 1 ;DNA (5'-D(TPCPCPAPCPGPGPGPTPAPYPYC)-3') ; × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPYPYTPAPCPCPCPGPTPGPGPA)-3') ; × 1 ;DNA (5'-D(TPCPCPAPCPGPGPGPTPAPYPYC)-3') ; × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3FMN7_BACPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–288； UniProt 1–285 Author chain B； PDBConstruct 4–288； UniProt 1–285

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5hlt
Deposition date deposition_date	2016-01-15
Structure title title	Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
Keywords keywords	Phenanthrene, Pyrene, DNA, Endonuclease, Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5hlt__assembly_1__model_1

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

Download this curve (.dat)

5hlt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hlt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.62 Å
Rg (electron density)	19.53 Å
Total Rg	20.38 Å
Atom count	2705
Residues	300
Excluded volume	46602 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hlt__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5hlt__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Restriction endonuclease R.BpuJI
Molecular weight formula_weight	33766.2 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	5417

GSHMNYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSNVNSHKS

Source Source

Source organism organism	Bacillus pumilus
NCBI taxonomy ID ncbi_taxonomy_id	1408
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPYPYTPAPCPCPCPGPTPGPGPA)-3') ;
Molecular weight formula_weight	3774.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L,C

GXTACCCGTGGA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPCPCPAPCPGPGPGPTPAPYPYC)-3') ;
Molecular weight formula_weight	3734.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,D

TCCACGGGTAXC

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5hltA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2080 —

Domain ID domain_id	5hltA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	5hltA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2090 —

Domain ID domain_id	5hltB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2080 —

Domain ID domain_id	5hltB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	5hltB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2090 —

▶

Unit-cell length a length_a	77.870 Å
Unit-cell length b length_b	85.503 Å
Unit-cell length c length_c	115.905 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	2.672 Å
Low-resolution limit resolution_low	46.491 Å
R factor r_factor	0.2030
R_work r_work	0.2007
R_free r_free	0.2436

Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain

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

Restriction endonuclease R.BpuJI

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

5hlt__assembly_1__model_1

5hlt__assembly_1__model_1 | I(q)

5hlt__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain

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

Restriction endonuclease R.BpuJI

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

5hlt__assembly_1__model_1

5hlt__assembly_1__model_1 | I(q)

5hlt__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)