SAXSdb — 5o79

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

OmpK36

Klebsiella pneumoniae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 22–365 Chain B； UniProt 22–365 Chain C； UniProt 22–365	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.08 M Magnesium Acetate tetrahydrate , 0.1 M sodium citrate, 14% w/v 5000 PEG MME	Resolution 1.65 Å R-free 0.190

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5O79	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NUP Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 22–365（344 aa） Chain B 22–365（344 aa） Chain C 22–365（344 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 19 LMT DODECYL-BETA-D-MALTOSIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.04 M magnesium chloride hexahydrate, 0.05 M sodium chloride, 0.1 M HEPES pH7.5 and 32 % PEG400	Resolution 2.90 Å R-free 0.290
6RD3 Crystal structure of the wild type OmpK36 from Klebsiella pneumonia Deposited 2019-04-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–365（344 aa） Chain B 22–365（344 aa） Chain C 22–365（344 aa）	Mutation：G0 Mutation：G0 Mutation：G0	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 17 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000	Resolution 1.98 Å R-free 0.234
6RD3 Crystal structure of the wild type OmpK36 from Klebsiella pneumonia Deposited 2019-04-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 22–365（344 aa） Chain E 22–365（344 aa） Chain F 22–365（344 aa）	Mutation：G0 Mutation：G0 Mutation：G0	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 12 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000	Resolution 1.98 Å R-free 0.234
7PZF Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia Deposited 2021-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–365（344 aa） Chain B 22–365（344 aa） Chain C 22–365（344 aa）	Mutation：T115 and D116 insertion Mutation：T115 and D116 insertion Mutation：T115 and D116 insertion	LI LITHIUM ION × 3 C14 TETRADECANE × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Lithium sulfate, 0.1 M Sodium citrate, and 10% PEG 4000 (pH 5.6)	Resolution 1.50 Å R-free 0.205
7PZF Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia Deposited 2021-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 22–365（344 aa） Chain E 22–365（344 aa） Chain F 22–365（344 aa）	Mutation：T115 and D116 insertion Mutation：T115 and D116 insertion Mutation：T115 and D116 insertion	LI LITHIUM ION × 6 C14 TETRADECANE × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Lithium sulfate, 0.1 M Sodium citrate, and 10% PEG 4000 (pH 5.6)	Resolution 1.50 Å R-free 0.205
7Q3T Crystal structure of the OmpK36 D insertion chimera from Klebsiella pneumonia Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–365（344 aa） Chain B 22–365（344 aa） Chain C 22–365（344 aa）	Mutation：D115 insertion Mutation：D115 insertion Mutation：D115 insertion	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 28 LI LITHIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Lithium sulfate, 0.1 M Sodium citrate, and 10% PEG 4000 (pH 5.6)	Resolution 1.79 Å R-free 0.213
7Q3T Crystal structure of the OmpK36 D insertion chimera from Klebsiella pneumonia Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 22–365（344 aa） Chain E 22–365（344 aa） Chain F 22–365（344 aa）	Mutation：D115 insertion Mutation：D115 insertion Mutation：D115 insertion	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 19 LI LITHIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Lithium sulfate, 0.1 M Sodium citrate, and 10% PEG 4000 (pH 5.6)	Resolution 1.79 Å R-free 0.213
7SZI Cryo-EM structure of OmpK36-TraN mating pair stabilization proteins from carbapenem-resistant Klebsiella pneumoniae Deposited 2021-11-27	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–365（344 aa） Chain B 22–365（344 aa） Chain C 22–365（344 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；SEC Buffer cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D6QLY0_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 22–365 Author chain B； PDBConstruct 1–344； UniProt 22–365 Author chain C； PDBConstruct 1–344； UniProt 22–365

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	5o79
Deposition date deposition_date	2017-06-08
Structure title title	Klebsiella pneumoniae OmpK36
Keywords keywords	Outer membrane protein, porin, ion transport, OmpC ortholog, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.89 Å
Radius of gyration Rg (electron density) rg_electron	30.32 Å
Forward intensity I(0) i0	220515000.00
Molecular weight molecular_weight	114100.0 kDa
Excluded volume excluded_volume	140640 Å³
Envelope volume envelope_volume	179800 Å³
Hydration-shell volume shell_volume	47491 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	39.26 Å
Envelope Rg envelope_rg	29.92 Å
Shape Rg shape_rg	30.33 Å
Total Rg total_rg	31.05 Å
Total atoms total_atoms	8084
Residues n_residues	1027
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.0 Å
Rg (real space) rg_real	30.65 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.2050e+08
I(0) uncertainty (real space) i0_real_error	2.9530e+06
Rg (reciprocal space) rg_reciprocal	30.76 Å
I(0) (reciprocal space) i0_reciprocal	220500000.0000
Solution quality estimate total_estimate	0.9083
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.5 Å
Skewness Skewness skewness	0.038
Kurtosis Kurtosis kurtosis	-0.636
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15920000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.946

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	OmpK36
Molecular weight formula_weight	38030.9 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	8724

AEIYNKDGNKLDLYGKIDGLHYFSDDKSVDGDQTYMRVGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEGATNNGRGWSKQNGDGFGTSLTYDIWDGISAGFAYSHSKRTDEQNSVPALGRGDNAETYTGGLKYDANNIYLASRYTQTYNATRAGSLGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLERGYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNSFTRNAGISTDDVVALGLVYQF

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI Class编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	635

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5o79a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.3 — Porins
Family Family family	f.4.3.1 — Porin

Domain ID domain_id	d5o79b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.3 — Porins
Family Family family	f.4.3.1 — Porin

Domain ID domain_id	d5o79c_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.3 — Porins
Family Family family	f.4.3.1 — Porin

CATH v4.4 (3 domains)

Domain ID domain_id	5o79A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5o79B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5o79C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

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8. Citations (1)

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Unit-cell length a length_a	232.316 Å
Unit-cell length b length_b	74.511 Å
Unit-cell length c length_c	90.814 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	107.570 Å
R factor r_factor	0.1483
R_work r_work	0.1461
R_free r_free	0.1896

fit	/app/data/saxs_computation/o7/5o79/5o79.fit
pddf	/app/data/pr_computation/o7/5o79/5o79.pr.out
profile	/app/data/saxs_computation/o7/5o79/5o79.dat

Klebsiella pneumoniae OmpK36

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

OmpK36

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction