SAXSdb — 3sys

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

Vanillate porin OpdK

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	1,2-ETHANEDIOL × 1 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 14 4-HYDROXY-3-METHOXYBENZOATE × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 3 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 15 4-HYDROXY-3-METHOXYBENZOATE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9HUR5_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 28–417 Author chain B； PDBConstruct 1–390； UniProt 28–417

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	3sys
Deposition date deposition_date	2011-07-18
Structure title title	Improved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK)
Keywords keywords	beta-barrel, channel, bacterial outer membrane, MEMBRANE PROTEIN; MEMBRANE 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.

3sys__assembly_1__model_1

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

Download this curve (.dat)

3sys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sys__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.08 Å
Rg (electron density)	21.32 Å
Total Rg	22.27 Å
Atom count	3086
Residues	374
Excluded volume	54736 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sys__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sys__assembly_2__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	Vanillate porin OpdK
Molecular weight formula_weight	43936.5 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	6853

AEGGFLEDAKTDLVLRNYYFNRDFRDHDAGKSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSGRGTSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSWGGHHHHHH

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	29

Entity 4 Entity 4 non-polymer

Description description	4-HYDROXY-3-METHOXYBENZOATE
Molecular weight formula_weight	167.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	667

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3sysa_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.7 — Outer membrane carboxylate (Occ) channels
Family Family family	f.4.7.2 — OccK-like (OprK-like)

Domain ID domain_id	d3sysb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.7 — Outer membrane carboxylate (Occ) channels
Family Family family	f.4.7.2 — OccK-like (OprK-like)

CATH v4.4 (2 domains)

Domain ID domain_id	3sysA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	3sysB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

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Unit-cell length a length_a	82.142 Å
Unit-cell length b length_b	96.840 Å
Unit-cell length c length_c	121.557 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	1.650 Å
Low-resolution limit resolution_low	19.907 Å
R factor r_factor	0.1816
R_work r_work	0.1813
R_free r_free	0.2007

Improved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK)

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

Vanillate porin OpdK

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

3sys__assembly_1__model_1

3sys__assembly_1__model_1 | I(q)

3sys__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Improved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK)

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

Vanillate porin OpdK

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

3sys__assembly_1__model_1

3sys__assembly_1__model_1 | I(q)

3sys__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)