SAXSdb — 4yrz

▼

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 monomer	Monomer	Protein 1	L-xylulofuranose-1,2-borate × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	L-xylulofuranose-1,2-borate × 1 water × 1	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 1–345； UniProt 21–365 Author chain B； PDBConstruct 1–345； UniProt 21–365

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	4yrz
Deposition date deposition_date	2015-03-16
Structure title title	Crystal Structure of LuxP In Complex With L-xylulofuranose-1,2-borate
Keywords keywords	PROTEIN-LIGAND COMPLEX, QUORUM SENSING, protein binding, signaling protein; SIGNALING PROTEIN
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.

4yrz__assembly_1__model_1

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

Download this curve (.dat)

4yrz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yrz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.09 Å
Rg (electron density)	20.18 Å
Total Rg	21.06 Å
Atom count	2728
Residues	339
Excluded volume	48281 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yrz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4yrz__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Autoinducer 2-binding periplasmic protein LuxP
Molecular weight formula_weight	39341.1 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	5643

GSMVLNGYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSDN

Source Source

Source organism organism	Vibrio harveyi
NCBI taxonomy ID ncbi_taxonomy_id	669
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	L-xylulofuranose-1,2-borate
Molecular weight formula_weight	192.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4yrza_
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	d4yrzb_
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

CATH v4.4 (4 domains)

Domain ID domain_id	4yrzA01
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	4yrzA02
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	4yrzB01
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	4yrzB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

▶

Unit-cell length a length_a	74.500 Å
Unit-cell length b length_b	85.036 Å
Unit-cell length c length_c	130.980 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.571 Å
Low-resolution limit resolution_low	49.187 Å
R factor r_factor	0.1745
R_work r_work	0.1705
R_free r_free	0.2244

Crystal Structure of LuxP In Complex With L-xylulofuranose-1,2-borate

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4yrz__assembly_1__model_1

4yrz__assembly_1__model_1 | I(q)

4yrz__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of LuxP In Complex With L-xylulofuranose-1,2-borate

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4yrz__assembly_1__model_1

4yrz__assembly_1__model_1 | I(q)

4yrz__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)