SAXSdb — 1mw9

▼

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

DNA Topoisomerase I

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 9 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOP1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–592； UniProt 1–592

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	1mw9
Deposition date deposition_date	2002-09-27
Structure title title	Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I
Keywords keywords	DNA TOPOISOMERASE, DECATENASE ENZYME, TOPRIM DOMAIN, ISOMERASE; ISOMERASE
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.

1mw9__assembly_1__model_1

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

Download this curve (.dat)

1mw9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mw9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.22 Å
Rg (electron density)	29.84 Å
Total Rg	30.30 Å
Atom count	4484
Residues	556
Excluded volume	79194 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mw9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA Topoisomerase I
Molecular weight formula_weight	66930.8 kDa
EC 编号 ec_number	5.99.1.2
Mutation mutation	H365R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	5265

MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENNLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQM

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	577

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1mw9x_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.10 — Prokaryotic type I DNA topoisomerase
Superfamily Superfamily superfamily	e.10.1 — Prokaryotic type I DNA topoisomerase
Family Family family	e.10.1.1 — Prokaryotic type I DNA topoisomerase

CATH v4.4 (4 domains)

Domain ID domain_id	1mw9X01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1mw9X02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	460 — Topoisomerase I; domain 2
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 2

Domain ID domain_id	1mw9X03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 3

Domain ID domain_id	1mw9X04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 4

▶

Unit-cell length a length_a	62.990 Å
Unit-cell length b length_b	78.705 Å
Unit-cell length c length_c	139.328 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.2089
R_work r_work	0.2084
R_free r_free	0.2164

Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I

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

DNA Topoisomerase I

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

1mw9__assembly_1__model_1

1mw9__assembly_1__model_1 | I(q)

1mw9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I

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

DNA Topoisomerase I

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

1mw9__assembly_1__model_1

1mw9__assembly_1__model_1 | I(q)

1mw9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)