3n9b

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

Method: X-RAY DIFFRACTION

▼

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

Probable ATP-dependent DNA ligase

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 CHLORIDE ION × 1 DI(HYDROXYETHYL)ETHER × 1 MANGANESE (II) ION × 1 YTTRIUM (III) ION × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 MANGANESE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I1X7_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 17–187 Author chain B； PDBConstruct 1–171； UniProt 17–187

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	3n9b
Deposition date deposition_date	2010-05-28
Structure title title	Crystal Structure of the P. aeruginosa LigD phosphoesterase domain
Keywords keywords	Phosphoesterase, Metalloenzyme, Ligase, NHEJ, Manganese, Beta Barrel; LIGASE
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.

3n9b__assembly_1__model_1

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

Download this curve (.dat)

3n9b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3n9b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.27 Å
Rg (electron density)	14.79 Å
Total Rg	16.21 Å
Atom count	1215
Residues	148
Excluded volume	21541 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3n9b__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3n9b__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 (7)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent DNA ligase
Molecular weight formula_weight	19475.0 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	2915

RQTPEPSGRKPRKDSTGLLRYCVQKHDASRLHYDFRLELDGTLKSWAVPKGPCLDPAVKRLAVQVEDHPLDYADFEGSIPQGHYGAGDVIVWDRGAWTPLDDPREGLEKGHLSFALDGEKLSGRWHLIRTNLRGKQSQWFLVKAKDGEARSLDRFDVLKERPDSVLSERTL

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	YTTRIUM (III) ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	358

▶

Unit-cell length a length_a	41.583 Å
Unit-cell length b length_b	45.550 Å
Unit-cell length c length_c	53.384 Å
Unit-cell angle α angle_alpha	102.32 °
Unit-cell angle β angle_beta	109.43 °
Unit-cell angle γ angle_gamma	104.59 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	37.395 Å
R factor r_factor	0.1527
R_work r_work	0.1475
R_free r_free	0.1988

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

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

Probable ATP-dependent DNA ligase

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

3n9b__assembly_1__model_1

3n9b__assembly_1__model_1 | I(q)

3n9b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

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

Probable ATP-dependent DNA ligase

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

3n9b__assembly_1__model_1

3n9b__assembly_1__model_1 | I(q)

3n9b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)