SAXSdb — 1s4i

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

superoxide dismutase-like protein yojM

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 CHLORIDE ION × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YOJM_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–175； UniProt 22–196 Author chain B； PDBConstruct 1–175； UniProt 22–196 Author chain C； PDBConstruct 1–175； UniProt 22–196 Author chain D； PDBConstruct 1–175； UniProt 22–196

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	1s4i
Deposition date deposition_date	2004-01-16
Structure title title	Crystal structure of a SOD-like protein from Bacillus subtilis
Keywords keywords	SOD, Cu-Zn SOD, SOD-like, superoxide dismutase, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1s4i__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1s4i__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1s4i__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	22.17 Å
Rg (electron density)	21.14 Å
Total Rg	21.91 Å
Atom count	2267
Residues	303
Excluded volume	39657 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1s4i__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1s4i__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1s4i__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1s4i__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1s4i__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1s4i__assembly_6__model_1`	dimeric （2）	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)

Entity 1 Entity 1 polymer

Description description	superoxide dismutase-like protein yojM
Molecular weight formula_weight	18738.8 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	4920

KPPDPPNRVPEKKVVETSAFGHHVQLVNREGKAVGFIEIKESDDEGLDIHISANSLRPGASLGFHIYEKGSCVRPDFESAGGPFNPLNKEHGFNNPMGHHAGDLPNLEVGADGKVDVIMNAPDTSLKKGSKLNILDEDGSAFIIHEQADDYLTNPSGNSGARIVCGALLGNNEKQ

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	390

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1s4ia_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.0 — automated matches

Domain ID domain_id	d1s4ib_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.0 — automated matches

Domain ID domain_id	d1s4ic_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.0 — automated matches

Domain ID domain_id	d1s4id_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	1s4iA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1s4iB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1s4iC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1s4iD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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Unit-cell length a length_a	38.225 Å
Unit-cell length b length_b	61.108 Å
Unit-cell length c length_c	64.915 Å
Unit-cell angle α angle_alpha	84.35 °
Unit-cell angle β angle_beta	76.02 °
Unit-cell angle γ angle_gamma	90.42 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	37.010 Å
R factor r_factor	0.2240
R_work r_work	0.2209
R_free r_free	0.2576

Crystal structure of a SOD-like protein from Bacillus subtilis

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

superoxide dismutase-like protein yojM

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

1s4i__assembly_5__model_1

1s4i__assembly_5__model_1 | I(q)

1s4i__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a SOD-like protein from Bacillus subtilis

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

superoxide dismutase-like protein yojM

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

1s4i__assembly_5__model_1

1s4i__assembly_5__model_1 | I(q)

1s4i__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)