SAXSdb — 3d5k

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

Outer membrane protein oprM

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SODIUM ION × 9 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPRM_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–468； UniProt 18–485 Author chain B； PDBConstruct 1–468； UniProt 18–485 Author chain C； PDBConstruct 1–468； UniProt 18–485

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	3d5k
Deposition date deposition_date	2008-05-16
Structure title title	Crystal structure of the OprM channel in a non-symmetrical space group
Keywords keywords	;membrane protein, channel, beta-alpha-barrel, Antibiotic resistance, Lipoprotein, Membrane, Outer membrane, Palmitate, Transmembrane, Transport ;; 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.

3d5k__assembly_1__model_1

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

Download this curve (.dat)

3d5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.54 Å
Rg (electron density)	39.45 Å
Total Rg	39.68 Å
Atom count	10480
Residues	1362
Excluded volume	185430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d5k__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein oprM
Molecular weight formula_weight	51779.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	11019

CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALENNRDLRVAALNVEAFRAQYRIQRADLFPRIGVDGSGTRQRLPGDLSTTGSPAISSQYGVTLGTTAWELDLFGRLRSLRDQALEQYLATEQAQRSAQTTLVASVATAYLTLKADQAQLQLTKDTLGTYQKSFDLTQRSYDVGVASALDLRQAQTAVEGARATLAQYTRLVAQDQNALVLLLGSGIPANLPQGLGLDQTLLTEVPAGLPSDLLQRRPDILEAEHQLMAANASIGAARAAFFPSISLTANAGTMSRQLSGLFDAGSGSWLFQPSINLPIFTAGSLRASLDYAKIQKDINVAQYEKAIQTAFQEVADGLAARGTFTEQLQAQRDLVKASDEYYQLADKRYRTGVDNYLTLLDAQRSLFTAQQQLITDRLNQLTSEVNLYKALGGGWNQQTVTQQQTAKKEDPQAHHHHHH

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	9

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	539

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3d5ka_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamily	f.5.1 — Outer membrane efflux proteins (OEP)
Family Family family	f.5.1.1 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	d3d5kb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamily	f.5.1 — Outer membrane efflux proteins (OEP)
Family Family family	f.5.1.1 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	d3d5kc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamily	f.5.1 — Outer membrane efflux proteins (OEP)
Family Family family	f.5.1.1 — Outer membrane efflux proteins (OEP)

CATH v4.4 (6 domains)

Domain ID domain_id	3d5kA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	3d5kA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	200 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	3d5kB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	3d5kB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	200 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	3d5kC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

Domain ID domain_id	3d5kC02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	200 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily	10 — Outer membrane efflux proteins (OEP)

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Unit-cell length a length_a	73.900 Å
Unit-cell length b length_b	70.200 Å
Unit-cell length c length_c	344.500 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	12

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2400
R_work r_work	0.2358
R_free r_free	0.2932

Crystal structure of the OprM channel in a non-symmetrical space group

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

Outer membrane protein oprM

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

3d5k__assembly_1__model_1

3d5k__assembly_1__model_1 | I(q)

3d5k__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the OprM channel in a non-symmetrical space group

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

Outer membrane protein oprM

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

3d5k__assembly_1__model_1

3d5k__assembly_1__model_1 | I(q)

3d5k__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)