SAXSdb — 7fvt

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

DNA gyrase subunit B,DNA gyrase subunit A Chimera

Staphylococcus aureus subsp. aureus N315

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(APGPCPCPGPTPAPGPGPGPCPCPCPTPAPCPGPGPCPT)-3') ; × 2 MANGANESE (II) ION × 3 CHLORIDE ION × 3 ;6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one ; × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYRB_STAAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–202； UniProt 410–644 Author chain B； PDBConstruct 2–202； UniProt 410–644

DNA gyrase subunit B,DNA gyrase subunit A Chimera

Staphylococcus aureus subsp. aureus N315

UniProt Q99XG5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(APGPCPCPGPTPAPGPGPGPCPCPCPTPAPCPGPGPCPT)-3') ; × 2 MANGANESE (II) ION × 3 CHLORIDE ION × 3 ;6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one ; × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYRA_STAAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 203–692； UniProt 2–491 Author chain B； PDBConstruct 203–692； UniProt 2–491

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	7fvt
Deposition date deposition_date	2023-04-18
Structure title title	Crystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1H-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4H-pyrido[3,2-b][1,4]oxazin-3-one
Keywords keywords	DNA GYRASE, TOPOISOMERASE;, ISOMERASE; 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.

7fvt__assembly_1__model_1

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

Download this curve (.dat)

7fvt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7fvt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.95 Å
Rg (electron density)	36.75 Å
Total Rg	37.12 Å
Atom count	11465
Residues	1381
Excluded volume	201040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7fvt__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 (6)

Entity 1 Entity 1 polymer

Description description	DNA gyrase subunit B,DNA gyrase subunit A Chimera
Molecular weight formula_weight	78109.0 kDa
EC 编号 ec_number	5.6.2.2
Mutation mutation	Y123F
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	12031

MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus N315
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APGPCPCPGPTPAPGPGPGPCPCPCPTPAPCPGPGPCPT)-3') ;
Molecular weight formula_weight	6136.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

AGCCGTAGGGCCCTACGGCT

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	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	;6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one ;
Molecular weight formula_weight	442.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	545

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7fvtA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	7fvtB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	92.938 Å
Unit-cell length b length_b	92.938 Å
Unit-cell length c length_c	407.651 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.081 Å
Low-resolution limit resolution_low	63.164 Å
R factor r_factor	0.2022
R_work r_work	0.1996
R_free r_free	0.2484

Crystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1H-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4H-pyrido[3,2-b][1,4]oxazin-3-one

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

DNA gyrase subunit B,DNA gyrase subunit A Chimera

State in the Current Structure

Other States of the Same Protein in the Database

DNA gyrase subunit B,DNA gyrase subunit A Chimera

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

7fvt__assembly_1__model_1

7fvt__assembly_1__model_1 | I(q)

7fvt__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1H-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4H-pyrido[3,2-b][1,4]oxazin-3-one

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

DNA gyrase subunit B,DNA gyrase subunit A Chimera

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 gyrase subunit B,DNA gyrase subunit A Chimera

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

7fvt__assembly_1__model_1

7fvt__assembly_1__model_1 | I(q)

7fvt__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)