SAXSdb — 1joe

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

AUTOINDUCER-2 PRODUCTION PROTEIN

Haemophilus influenzae Rd

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 2 ZINC ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 2 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LUXS_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167 Author chain B； PDBConstruct 1–167； UniProt 1–167 Author chain C； PDBConstruct 1–167； UniProt 1–167 Author chain D； PDBConstruct 1–167； UniProt 1–167

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	1joe
Deposition date deposition_date	2001-07-27
Structure title title	Crystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae
Keywords keywords	LuxS, HI0491, structural genomics, twinned crystal, Structure 2 Function Project, S2F, SIGNALING PROTEIN; SIGNALING 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.

1joe__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1joe__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1joe__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.13 Å
Rg (electron density)	18.18 Å
Total Rg	18.99 Å
Atom count	2294
Residues	296
Excluded volume	40910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1joe__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1joe__assembly_2__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	AUTOINDUCER-2 PRODUCTION PROTEIN
Molecular weight formula_weight	18548.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4722

MPLLDSFKVDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKNEDLSLDNSLLK

Source Source

Source organism organism	Haemophilus influenzae Rd
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	134

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1joea_
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

Domain ID domain_id	d1joeb_
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

Domain ID domain_id	d1joec_
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

Domain ID domain_id	d1joed_
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 (4 domains)

Domain ID domain_id	1joeA00
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)

Domain ID domain_id	1joeB00
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)

Domain ID domain_id	1joeC00
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)

Domain ID domain_id	1joeD00
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	115.530 Å
Unit-cell length b length_b	115.530 Å
Unit-cell length c length_c	51.230 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	16

Space group space_group	P 42
Space-group number int_tables_number	77
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2099
R_work r_work	0.2053
R_free r_free	0.2992

Crystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae

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

AUTOINDUCER-2 PRODUCTION PROTEIN

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

1joe__assembly_2__model_1

1joe__assembly_2__model_1 | I(q)

1joe__assembly_2__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 Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae

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

AUTOINDUCER-2 PRODUCTION PROTEIN

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

1joe__assembly_2__model_1

1joe__assembly_2__model_1 | I(q)

1joe__assembly_2__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)