3b4s

Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633

Method: X-RAY DIFFRACTION

▼

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

Protein LuxT

Vibrio parahaemolyticus RIMD 2210633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87J33_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–94； UniProt 63–153 Author chain B； PDBConstruct 4–94； UniProt 63–153 Author chain C； PDBConstruct 4–94； UniProt 63–153 Author chain D； PDBConstruct 4–94； UniProt 63–153 Author chain E； PDBConstruct 4–94； UniProt 63–153 Author chain F； PDBConstruct 4–94； UniProt 63–153 Author chain G； PDBConstruct 4–94； UniProt 63–153 Author chain H； PDBConstruct 4–94； UniProt 63–153

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3b4s
Deposition date deposition_date	2007-10-24
Structure title title	Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633
Keywords keywords	;APC91483.1, LuxT domain, Vibrio parahaemolyticus RIMD 2210633, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3b4s__assembly_1__model_1

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

Download this curve (.dat)

3b4s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b4s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.00 Å
Rg (electron density)	25.02 Å
Total Rg	25.78 Å
Atom count	4455
Residues	531
Excluded volume	79836 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b4s__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3b4s__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (1)

▼

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3b4sA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	790 — luxt domain from vibrio parahaemolyticus

Domain ID domain_id	3b4sH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	830 — luxt domain from vibrio parahaemolyticus

▶

Unit-cell length a length_a	147.438 Å
Unit-cell length b length_b	147.438 Å
Unit-cell length c length_c	382.487 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	144

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.220 Å
R factor r_factor	0.1924
R_work r_work	0.1902
R_free r_free	0.2322

Description description	Protein LuxT
Molecular weight formula_weight	10917.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	5906

Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633

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

Protein LuxT

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

3b4s__assembly_1__model_1

3b4s__assembly_1__model_1 | I(q)

3b4s__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Source organism organism	Vibrio parahaemolyticus RIMD 2210633
NCBI taxonomy ID ncbi_taxonomy_id	223926
Host organism host_organism	Escherichia coli BL21

Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633

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

Protein LuxT

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

3b4s__assembly_1__model_1

3b4s__assembly_1__model_1 | I(q)

3b4s__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)