5cdr

2.65 structure of S.aureus DNA gyrase and artificially nicked DNA

Method: X-RAY DIFFRACTION

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

DNA gyrase subunit A

Staphylococcus aureus (strain N315)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 3	DNA gyrase subunit B,DNA gyrase subunit B × 2 （P66937） ;DNA (5'-D(APGPCPCPGPTPAP)-3') ; × 1 ;DNA (5'-D(GPGPTPAPCPCPTPAPCPGPGPCPT)-3') ; × 1 ;DNA (5'-D(APGPCPCPGPTPAPGPGPTPAPCPCPTPAPCPGPGPCP*T)-3') ; × 1 MANGANESE (II) ION × 3 GLYCEROL × 6 water × 7	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 1–483； UniProt 9–491 Author chain C； PDBConstruct 1–483； UniProt 9–491

DNA gyrase subunit B,DNA gyrase subunit B

Staphylococcus aureus (strain N315)

UniProt P66937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 3	DNA gyrase subunit A × 2 （Q99XG5） ;DNA (5'-D(APGPCPCPGPTPAP)-3') ; × 1 ;DNA (5'-D(GPGPTPAPCPCPTPAPCPGPGPCPT)-3') ; × 1 ;DNA (5'-D(APGPCPCPGPTPAPGPGPTPAPCPCPTPAPCPGPGPCP*T)-3') ; × 1 MANGANESE (II) ION × 3 GLYCEROL × 6 water × 7	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–127； UniProt 417–543 Author chain B； PDBConstruct 130–190； UniProt 580–640 Author chain D； PDBConstruct 1–127； UniProt 417–543 Author chain D； PDBConstruct 130–190； UniProt 580–640

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	5cdr
Deposition date deposition_date	2015-07-04
Structure title title	2.65 structure of S.aureus DNA gyrase and artificially nicked DNA
Keywords keywords	TYPE IIA 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.

5cdr__assembly_1__model_1

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

Download this curve (.dat)

5cdr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cdr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.41 Å
Rg (electron density)	37.11 Å
Total Rg	37.48 Å
Atom count	11395
Residues	1379
Excluded volume	200050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cdr__assembly_1__model_1`	heptameric （7）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA gyrase subunit A
Molecular weight formula_weight	54738.5 kDa
EC 编号 ec_number	5.99.1.3
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,C
Atom count atom_count	12435

INERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG

Source Source

Source organism organism	Staphylococcus aureus (strain N315)
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA gyrase subunit B,DNA gyrase subunit B
Molecular weight formula_weight	21345.3 kDa
EC 编号 ec_number	5.99.1.3,5.99.1.3
Mutation mutation	;GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG ;
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA

Source Source

Source organism organism	Staphylococcus aureus (strain N315)
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APGPCPCPGPTPAP)-3') ;
Molecular weight formula_weight	2451.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AGCCGTAG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(GPGPTPAPCPCPTPAPCPGPGPCP*T)-3') ;
Molecular weight formula_weight	3967.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GGTACCTACGGCT

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(APGPCPCPGPTPAPGPGPTPAPCPCPTPAPCPGPGPCPT)-3') ;
Molecular weight formula_weight	6135.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AGCCGTAGGTACCTACGGCT

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	644

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5cdrB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	5cdrD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

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Unit-cell length a length_a	93.395 Å
Unit-cell length b length_b	93.395 Å
Unit-cell length c length_c	410.583 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	2.650 Å
Low-resolution limit resolution_low	39.740 Å
R factor r_factor	0.1888
R_work r_work	0.1879
R_free r_free	0.2097

2.65 structure of S.aureus DNA gyrase and artificially nicked DNA

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

DNA gyrase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

DNA gyrase subunit B,DNA gyrase subunit B

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

5cdr__assembly_1__model_1

5cdr__assembly_1__model_1 | I(q)

5cdr__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

2.65 structure of S.aureus DNA gyrase and artificially nicked DNA

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

DNA gyrase 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 gyrase subunit B,DNA gyrase subunit B

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

5cdr__assembly_1__model_1

5cdr__assembly_1__model_1 | I(q)

5cdr__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)