SAXSdb — 5xt6

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

Zinc-dependent sulfurtransferase SufU

Bacillus subtilis (strain 168)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cysteine desulfurase SufS × 2 （O32164） ZINC ION × 2 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUFU_BACSU
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain D； PDBConstruct 1–147； UniProt 1–147 Author chain C； PDBConstruct 1–147； UniProt 1–147

Cysteine desulfurase SufS

Bacillus subtilis (strain 168)

UniProt O32164

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Zinc-dependent sulfurtransferase SufU × 1 （O32163） Zinc-dependent sulfurtransferase SufU × 1 （O32163） ZINC ION × 2 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUFS_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–409； UniProt 1–406 Author chain B； PDBConstruct 4–409； UniProt 1–406

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	5xt6
Deposition date deposition_date	2017-06-17
Structure title title	A sulfur-transferring catalytic intermediate of SufS-SufU complex from Bacillus subtilis
Keywords keywords	Iron-sulfur cluster biosynthesis, SUF machinery, Cysteine desulfurase, Sulfur mobilization, Metalloprotein, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

5xt6__assembly_1__model_1

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

Download this curve (.dat)

5xt6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xt6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.92 Å
Rg (electron density)	31.00 Å
Total Rg	31.64 Å
Atom count	8440
Residues	1079
Excluded volume	150140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xt6__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	Zinc-dependent sulfurtransferase SufU
Molecular weight formula_weight	17256.6 kDa
EC 编号 ec_number	2.-.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	8443

MSFNANLDTLYRQVIMDHYKNPRNKGVLNDSIVVDMNNPTCGDRIRLTMKLDGDIVEDAKFEGEGCSISMASASMMTQAIKGKDIETALSMSKIFSDMMQGKEYDDSIDLGDIEALQGVSKFPARIKCATLSWKALEKGVAKEEGGNLEHHHHHH

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cysteine desulfurase SufS
Molecular weight formula_weight	46618.6 kDa
EC 编号 ec_number	2.8.1.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGHMNITDIREQFPILHQQVNGHDLVYLDSAATSQKPRAVIETLDKYYNQYNSNVHRGVHTLGTRATDGYEGAREKVRKFINAKSMAEIIFTKGTTTSLNMVALSYARANLKPGDEVVITYMEHHANIIPWQQAVKATGATLKYIPLQEDGTISLEDVRETVTSNTKIVAVSHVSNVLGTVNPIKEMAKIAHDNGAVIVVDGAQSTPHMKIDVQDLDCDFFALSSHKMCGPTGVGVLYGKKALLENMEPAEFGGEMIDFVGLYESTWKELPWKFEAGTPIIAGAIGLGAAIDFLEEIGLDEISRHEHKLAAYALERFRQLDGVTVYGPEERAGLVTFNLDDVHPHDVATVLDAEGIAVRAGHHCAQPLMKWLDVTATARASFYLYNTEEEIDKLVEALQKTKEYFTNVFVDLEHHHHHH

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Zinc-dependent sulfurtransferase SufU
Molecular weight formula_weight	17288.7 kDa
EC 编号 ec_number	2.-.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSFNANLDTLYRQVIMDHYKNPRNKGVLNDSIVVDMNNPTCGDRIRLTMKLDGDIVEDAKFEGEGCSISMASASMMTQAIKGKDIETALSMSKIFSDMMQGKEYDDSIDLGDIEALQGVSKFPARIKCATLSWKALEKGVAKEEGGNLEHHHHHH

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID
Molecular weight formula_weight	320.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5xt6A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	5xt6B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	5xt6C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1010 — Sufe protein. Chain: A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5xt6D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1010 — Sufe protein. Chain: A
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	73.930 Å
Unit-cell length b length_b	73.930 Å
Unit-cell length c length_c	367.740 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	48.290 Å
R factor r_factor	0.2248
R_work r_work	0.2228
R_free r_free	0.2621

A sulfur-transferring catalytic intermediate of SufS-SufU complex from Bacillus subtilis

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

Zinc-dependent sulfurtransferase SufU

State in the Current Structure

Other States of the Same Protein in the Database

Cysteine desulfurase SufS

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

5xt6__assembly_1__model_1

5xt6__assembly_1__model_1 | I(q)

5xt6__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

A sulfur-transferring catalytic intermediate of SufS-SufU complex from Bacillus subtilis

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

Zinc-dependent sulfurtransferase SufU

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cysteine desulfurase SufS

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

5xt6__assembly_1__model_1

5xt6__assembly_1__model_1 | I(q)

5xt6__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)