2hj9

Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ

Method: X-RAY DIFFRACTION

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

Autoinducer 2-binding periplasmic protein luxP

Vibrio harveyi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Autoinducer 2 sensor kinase/phosphatase luxQ × 2 （P54302） 3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2,2,6,6A-TETRAOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LUXP_VIBHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–339； UniProt 27–365 Author chain B； PDBConstruct 1–339； UniProt 27–365

Autoinducer 2 sensor kinase/phosphatase luxQ

Vibrio harveyi

UniProt P54302

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Autoinducer 2-binding periplasmic protein luxP × 2 （P54300） 3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2,2,6,6A-TETRAOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LUXQ_VIBHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–221； UniProt 53–271 Author chain D； PDBConstruct 3–221； UniProt 53–271

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	2hj9
Deposition date deposition_date	2006-06-30
Structure title title	Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ
Keywords keywords	;PERIPLASMIC BINDING PROTEIN, PER/ARNT/SIMPLE-MINDED (PAS) FOLD, AUTOINDUCER-2 (AI-2), QUORUM SENSING, HISTIDINE SENSOR KINASE, 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.

2hj9__assembly_1__model_1

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

Download this curve (.dat)

2hj9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hj9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.02 Å
Rg (electron density)	33.51 Å
Total Rg	34.13 Å
Atom count	8698
Residues	1081
Excluded volume	154060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hj9__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 (4)

Entity 1 Entity 1 polymer

Description description	Autoinducer 2-binding periplasmic protein luxP
Molecular weight formula_weight	38739.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9092

GYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSDN

Source Source

Source organism organism	Vibrio harveyi
NCBI taxonomy ID ncbi_taxonomy_id	669
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Autoinducer 2 sensor kinase/phosphatase luxQ
Molecular weight formula_weight	24868.9 kDa
EC 编号 ec_number	3.1.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSKQQTSALIHNIFDSHFAAIQIHHDSNSKSEVIRDFYTDRDTDVLNFFFLSIDQSDPSHTPEFRFLTDHKGIIWDDGNAHFYGVNDLILDSLANRVSFSNNWYYINVMTSIGSRHMLVRRVPILDPSTGEVLGFSFNAVVLDNNFALMEKLKSESNVDNVVLVANSVPLANSLIGDEPYNVADVLQRKSSDKRLDKLLVIETPIVVNAVTTELCLLTVQD

Source Source

Source organism organism	Vibrio harveyi
NCBI taxonomy ID ncbi_taxonomy_id	669
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2,2,6,6A-TETRAOL
Molecular weight formula_weight	192.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	394

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hj9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.1 — L-arabinose binding protein-like

Domain ID domain_id	d2hj9b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.1 — L-arabinose binding protein-like

Domain ID domain_id	d2hj9c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.3 — LuxQ-periplasmic domain-like

Domain ID domain_id	d2hj9d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.3 — LuxQ-periplasmic domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	2hj9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2hj9A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2hj9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2hj9B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2hj9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	220 — LuxQ periplasmic domain, N-terminal subdomain

Domain ID domain_id	2hj9C02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	20 — Anthopleurin-A
Homologous superfamily homologous superfamily	100 — LuxQ periplasmic domain, C-terminal subdomain

Domain ID domain_id	2hj9D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	220 — LuxQ periplasmic domain, N-terminal subdomain

Domain ID domain_id	2hj9D02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	20 — Anthopleurin-A
Homologous superfamily homologous superfamily	100 — LuxQ periplasmic domain, C-terminal subdomain

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Unit-cell length a length_a	83.916 Å
Unit-cell length b length_b	83.916 Å
Unit-cell length c length_c	365.328 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.340 Å
Low-resolution limit resolution_low	29.700 Å
R factor r_factor	0.2097
R_work r_work	0.2069
R_free r_free	0.2618

Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ

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

Autoinducer 2-binding periplasmic protein luxP

State in the Current Structure

Other States of the Same Protein in the Database

Autoinducer 2 sensor kinase/phosphatase luxQ

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

2hj9__assembly_1__model_1

2hj9__assembly_1__model_1 | I(q)

2hj9__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ

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

Autoinducer 2-binding periplasmic protein luxP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Autoinducer 2 sensor kinase/phosphatase luxQ

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

2hj9__assembly_1__model_1

2hj9__assembly_1__model_1 | I(q)

2hj9__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)