SAXSdb — 2r2d

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

Zn-dependent hydrolases

Agrobacterium tumefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 PHOSPHATE ION × 3 GLYCEROL × 4 water × 2	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 PHOSPHATE ION × 4 GLYCEROL × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 PHOSPHATE ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 PHOSPHATE ION × 9 GLYCEROL × 10 water × 6	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 1 GLYCEROL × 3 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 2 GLYCEROL × 2 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	ZINC ION × 2 PHOSPHATE ION × 2 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CKY2_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 1–276 Author chain B； PDBConstruct 1–276； UniProt 1–276 Author chain C； PDBConstruct 1–276； UniProt 1–276 Author chain D； PDBConstruct 1–276； UniProt 1–276 Author chain E； PDBConstruct 1–276； UniProt 1–276 Author chain F； PDBConstruct 1–276； UniProt 1–276

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	2r2d
Deposition date deposition_date	2007-08-24
Structure title title	Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens
Keywords keywords	;lactonase, N-acyl hompserine lactone, di-nuclear zinc center, quorum quenching, AiiB, phosphate, Agrobacterium tumefaciens, 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.

2r2d__assembly_1__model_1

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

Download this curve (.dat)

2r2d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r2d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.88 Å
Rg (electron density)	26.49 Å
Total Rg	27.24 Å
Atom count	4351
Residues	552
Excluded volume	76605 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r2d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r2d__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2r2d__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2r2d__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2r2d__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2r2d__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2r2d__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2r2d__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2r2d__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2r2d__assembly_10__model_1`	monomeric （1）	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	Zn-dependent hydrolases
Molecular weight formula_weight	30596.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15215

MGNKLFVLDLGEIRVDENFIIANSTFVTPQKPTVSSRLIDIPVSAYLIQCTDATVLYDTGCHPECMGTNGRWPAQSQLNAPYIGASECNLPERLRQLGLSPDDISTVVLSHLHNDHAGCVEYFGKSRLIAHEDEFATAVRYFATGDHSSPYIVKDIEAWLATPRNWDLVGRDERERELAPGVNLLNFGTGHASGMLGLAVRLEKQPGFLLVSDACYTATNYGPPARRAGVLHDTIGYDRTVSHIRQYAESRSLTVLFGHDREQFASLIKSTDGFYE

Source Source

Source organism organism	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1521

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2r2dA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2r2dB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2r2dC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2r2dD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2r2dE00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2r2dF00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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Unit-cell length a length_a	79.146 Å
Unit-cell length b length_b	158.033 Å
Unit-cell length c length_c	80.439 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	18.100 Å
R factor r_factor	0.1617
R_work r_work	0.1590
R_free r_free	0.2127

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens

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

Zn-dependent hydrolases

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

2r2d__assembly_1__model_1

2r2d__assembly_1__model_1 | I(q)

2r2d__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens

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

Zn-dependent hydrolases

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

2r2d__assembly_1__model_1

2r2d__assembly_1__model_1 | I(q)

2r2d__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)