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4tma

Crystal structure of gyrase bound to its inhibitor YacG

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA gyrase subunit A

Escherichia coli

UniProt U6NB78

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit B × 2 （U6NGU8） DNA gyrase inhibitor YacG × 2 （P0A8H8） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit B × 2 （U6NGU8） DNA gyrase inhibitor YacG × 2 （P0A8H8） ZINC ION × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4tma 4tma

2 assemblies

View Construct and Data Evidence
UniProt name U6NB78_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–525； UniProt 1–525 Author chain C； PDBConstruct 1–525； UniProt 1–525 Author chain E； PDBConstruct 1–525； UniProt 1–525 Author chain G； PDBConstruct 1–525； UniProt 1–525

DNA gyrase subunit B

Escherichia coli

UniProt U6NGU8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit A × 2 （U6NB78） DNA gyrase inhibitor YacG × 2 （P0A8H8） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit A × 2 （U6NB78） DNA gyrase inhibitor YacG × 2 （P0A8H8） ZINC ION × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4tma 4tma

2 assemblies

View Construct and Data Evidence
UniProt name U6NGU8_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–417； UniProt 388–801 Author chain D； PDBConstruct 4–417； UniProt 388–801 Author chain F； PDBConstruct 4–417； UniProt 388–801 Author chain H； PDBConstruct 4–417； UniProt 388–801

DNA gyrase inhibitor YacG

Escherichia coli

UniProt P0A8H8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit A × 2 （U6NB78） DNA gyrase subunit B × 2 （U6NGU8） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 DNA gyrase subunit A × 2 （U6NB78） DNA gyrase subunit B × 2 （U6NGU8） ZINC ION × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1lv3

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4tma 4tma

2 assemblies

View Construct and Data Evidence
UniProt name YACG_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 1–65； UniProt 1–65 Author chain J； PDBConstruct 1–65； UniProt 1–65 Author chain K； PDBConstruct 1–65； UniProt 1–65 Author chain L； PDBConstruct 1–65； UniProt 1–65

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_id4tma
Deposition date deposition_date2014-05-31
Structure title titleCrystal structure of gyrase bound to its inhibitor YacG
Keywords keywordsIsomerase, DUF329, ISOMERASE-ISOMERASE INHIBITOR complex; ISOMERASE/ISOMERASE INHIBITOR
Experimental Method methodX-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.

4tma__assembly_1__model_1

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

Download this curve (.dat)

4tma__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4tma__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）40.69 Å
Rg (electron density)39.98 Å
Total Rg40.41 Å
Atom count13497
Residues1707
Excluded volume240460 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4tma__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4tma__assembly_2__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 (4)

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id4tmaA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id4tmaA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
Domain ID domain_id4tmaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id4tmaB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily370 —
Domain ID domain_id4tmaB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily690 —
Domain ID domain_id4tmaC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id4tmaC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
Domain ID domain_id4tmaD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id4tmaE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id4tmaE03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
Domain ID domain_id4tmaF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id4tmaF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily370 —
Domain ID domain_id4tmaF03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily690 —
Domain ID domain_id4tmaG01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id4tmaG03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
Domain ID domain_id4tmaH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id4tmaI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id4tmaJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id4tmaK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id4tmaL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
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7. Citations (1)