2wyf

Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution

Method: X-RAY DIFFRACTION

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

PA-I GALACTOPHILIC LECTIN

PSEUDOMONAS AERUGINOSA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 1	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 1 CALCIUM ION × 2 alpha-D-galactopyranose × 1 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 2 CALCIUM ION × 2 water × 2	Consistent with protein count
3	Other combination	Homooligomer	Protein 2 其他Polymer 1	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 1 CALCIUM ION × 2 alpha-D-galactopyranose × 1 water × 2	Consistent with protein count
4	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 2 CALCIUM ION × 2 water × 2	Consistent with protein count
5	Other combination	Homooligomer	Protein 4 其他Polymer 3	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 3 CALCIUM ION × 4 alpha-D-galactopyranose × 1 water × 4	Consistent with protein count
6	Other combination	Homooligomer	Protein 4 其他Polymer 3	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside × 3 CALCIUM ION × 4 alpha-D-galactopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA1L_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 2–122 Author chain B； PDBConstruct 1–121； UniProt 2–122 Author chain C； PDBConstruct 1–121； UniProt 2–122 Author chain D； PDBConstruct 1–121； UniProt 2–122 Author chain E； PDBConstruct 1–121； UniProt 2–122 Author chain F； PDBConstruct 1–121； UniProt 2–122 Author chain G； PDBConstruct 1–121； UniProt 2–122 Author chain H； PDBConstruct 1–121； UniProt 2–122

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	2wyf
Deposition date deposition_date	2009-11-16
Structure title title	Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution
Keywords keywords	SUGAR BINDING PROTEIN, LECTIN; SUGAR BINDING 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.

2wyf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2wyf__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wyf__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.10 Å
Rg (electron density)	17.97 Å
Total Rg	18.89 Å
Atom count	1838
Residues	242
Excluded volume	32368 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wyf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wyf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wyf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2wyf__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2wyf__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2wyf__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Description description	PA-I GALACTOPHILIC LECTIN
Molecular weight formula_weight	12770.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	8007

AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS

Source Source

Source organism organism	PSEUDOMONAS AERUGINOSA
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	alpha-D-galactopyranose-(1-2)-methyl beta-D-galactopyranoside
Molecular weight formula_weight	356.3 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	alpha-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	646

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2wyfa_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfb_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfc_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfd_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfe_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyff_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfg_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d2wyfh_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

CATH v4.4 (8 domains)

Domain ID domain_id	2wyfA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	2wyfH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

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Unit-cell length a length_a	49.885 Å
Unit-cell length b length_b	99.788 Å
Unit-cell length c length_c	91.318 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	89.800 Å
R factor r_factor	0.1704
R_work r_work	0.1657
R_free r_free	0.2589

Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution

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

PA-I GALACTOPHILIC LECTIN

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

2wyf__assembly_3__model_1

2wyf__assembly_3__model_1 | I(q)

2wyf__assembly_3__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution

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

PA-I GALACTOPHILIC LECTIN

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

2wyf__assembly_3__model_1

2wyf__assembly_3__model_1 | I(q)

2wyf__assembly_3__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)