8qmb

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

Method: X-RAY DIFFRACTION

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

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

Streptococcus pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(TPGPTPGPGPAPT)-3') ; × 1 ;DNA (5'-D(PGPGPTPTPAPTPCPCPAPCPA)-3') ; × 1 ;DNA (5'-D(GPTPAPAPTPAPC)-3') ; × 1 ;DNA (5'-D(PAPAPCPCPGPTPAPTPTPAPC)-3') ; × 1 MAGNESIUM ION × 6 CHLORIDE ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 MALONIC ACID × 2 ACETATE ION × 4 FORMIC ACID × 4 delafloxacin × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARC_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 247–734； UniProt 1–488 Author chain B； PDBConstruct 247–734； UniProt 1–488

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

Streptococcus pneumoniae

UniProt Q59961

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(TPGPTPGPGPAPT)-3') ; × 1 ;DNA (5'-D(PGPGPTPTPAPTPCPCPAPCPA)-3') ; × 1 ;DNA (5'-D(GPTPAPAPTPAPC)-3') ; × 1 ;DNA (5'-D(PAPAPCPCPGPTPAPTPTPAPC)-3') ; × 1 MAGNESIUM ION × 6 CHLORIDE ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 MALONIC ACID × 2 ACETATE ION × 4 FORMIC ACID × 4 delafloxacin × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARE_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–245； UniProt 404–647 Author chain B； PDBConstruct 2–245； UniProt 404–647

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	8qmb
Deposition date deposition_date	2023-09-21
Structure title title	Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin
Keywords keywords	;PROTEIN-DNA CLEAVAGE COMPLEX, TOPOISOMERASE IIA, DELAFLOXACIN, TOPOISOMERASE IV-DNA-ANTIBIOTIC COMPLEX, ISOMERASE, PEGylated GRAPHENE ;; ISOMERASE
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.

8qmb__assembly_1__model_1

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

Download this curve (.dat)

8qmb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qmb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.73 Å
Rg (electron density)	36.67 Å
Total Rg	37.13 Å
Atom count	24575
Residues	1484
Excluded volume	218840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qmb__assembly_1__model_1`	hexameric （6）	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 (13)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
Molecular weight formula_weight	84211.4 kDa
EC 编号 ec_number	5.6.2.2
Mutation mutation	Insertion of His at postion 648
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	25726

MKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEEATVFHMSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKALEHHHHHH

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPGPTPGPGPAPT)-3') ;
Molecular weight formula_weight	2168.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TGTGGAT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPGPTPTPAPTPCPCPAPCP*A)-3') ;
Molecular weight formula_weight	3333.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GGTTATCCACA

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(GPTPAPAPTPAPC)-3') ;
Molecular weight formula_weight	2121.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GTAATAC

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(PAPAPCPCPGPTPAPTPTPAP*C)-3') ;
Molecular weight formula_weight	3317.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

AACCGTATTAC

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

Description description	delafloxacin
Molecular weight formula_weight	440.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1059

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Unit-cell length a length_a	157.215 Å
Unit-cell length b length_b	157.215 Å
Unit-cell length c length_c	211.948 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	83.628 Å
R factor r_factor	—
R_work r_work	0.1687
R_free r_free	0.2064

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

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

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

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

8qmb__assembly_1__model_1

8qmb__assembly_1__model_1 | I(q)

8qmb__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 (13)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

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

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

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

8qmb__assembly_1__model_1

8qmb__assembly_1__model_1 | I(q)

8qmb__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 (13)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)