SAXSdb — 1ycl

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

S-ribosylhomocysteinase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 2 SULFATE ION × 2 (S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LUXS_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 2–157

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	1ycl
Deposition date deposition_date	2004-12-22
Structure title title	Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate
Keywords keywords	Quorum Sensing, metalloenzyme, HYDROLASE; HYDROLASE
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.

1ycl__assembly_1__model_1

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

Download this curve (.dat)

1ycl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ycl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.48 Å
Rg (electron density)	18.34 Å
Total Rg	19.19 Å
Atom count	2486
Residues	308
Excluded volume	44183 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ycl__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	S-ribosylhomocysteinase
Molecular weight formula_weight	17575.0 kDa
EC 编号 ec_number	3.13.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1346

PSVESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDIIDISPMGAQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEELLKVFG

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID
Molecular weight formula_weight	267.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ycla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.2 — Autoinducer-2 production protein LuxS

CATH v4.4 (1 domains)

Domain ID domain_id	1yclA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	80 — S-ribosylhomocysteinase (LuxS)

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Unit-cell length a length_a	62.530 Å
Unit-cell length b length_b	62.530 Å
Unit-cell length c length_c	149.650 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 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	16.050 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2560

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

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

S-ribosylhomocysteinase

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

1ycl__assembly_1__model_1

1ycl__assembly_1__model_1 | I(q)

1ycl__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

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

S-ribosylhomocysteinase

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

1ycl__assembly_1__model_1

1ycl__assembly_1__model_1 | I(q)

1ycl__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)