SAXSdb — 5nup

▼

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 22–365 Chain B； UniProt 22–365 Chain C； UniProt 22–365	Not recorded	ABC transporter permease × 3 （A0A0W8AQT6） 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

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 5NUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5O79 Klebsiella pneumoniae OmpK36 Deposited 2017-06-08	Different oligomeric state 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）	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
6RD3 Crystal structure of the wild type OmpK36 from Klebsiella pneumonia Deposited 2019-04-12	Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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

ABC transporter permease

Klebsiella pneumoniae

UniProt A0A0W8AQT6

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 18–253 Chain E； UniProt 18–253 Chain F； UniProt 18–253	Not recorded	OmpK36 × 3 （D6QLY0） 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

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 5NUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NUO Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 18–253（236 aa） Chain D 18–253（236 aa） Chain F 18–253（236 aa）	Not recorded	SO4 SULFATE ION × 6 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400	Resolution 3.20 Å R-free 0.269
5NUR 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 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 18–253（236 aa） Chain D 18–253（236 aa） Chain F 18–253（236 aa）	Not recorded	CA CALCIUM ION × 3 SO4 SULFATE ION × 8 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400	Resolution 3.29 Å R-free 0.259

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0W8AQT6_KLEPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–236； UniProt 18–253 Author chain E； PDBConstruct 1–236； UniProt 18–253 Author chain F； PDBConstruct 1–236； UniProt 18–253

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	5nup
Deposition date deposition_date	2017-05-01
Structure title title	Structural basis for maintenance of bacterial outer membrane lipid asymmetry
Keywords keywords	Outer membrane, lipid asymmetry, lipoprotein, phospholipid translocation, membrane protein; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.20 Å
Radius of gyration Rg (electron density) rg_electron	42.50 Å
Forward intensity I(0) i0	523868000.00
Molecular weight molecular_weight	186990.0 kDa
Excluded volume excluded_volume	233330 Å³
Envelope volume envelope_volume	319280 Å³
Hydration-shell volume shell_volume	64354 Å³
Envelope diameter envelope_diameter	146.0 Å
Shell Rg shell_rg	45.84 Å
Envelope Rg envelope_rg	42.83 Å
Shape Rg shape_rg	42.50 Å
Total Rg total_rg	42.66 Å
Total atoms total_atoms	13238
Residues n_residues	1592
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

▼

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

Maximum dimension Dmax dmax	141.4 Å
Rg (real space) rg_real	42.29 Å
Rg uncertainty (real space) rg_real_error	1.78 Å
I(0) (real space) i0_real	5.2390e+08
I(0) uncertainty (real space) i0_real_error	9.8090e+06
Rg (reciprocal space) rg_reciprocal	42.20 Å
I(0) (reciprocal space) i0_reciprocal	523800000.0000
Solution quality estimate total_estimate	0.8114
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.7 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48340000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

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	13238

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

Entity 2 Entity 2 polymer

Description description	ABC transporter permease
Molecular weight formula_weight	26364.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

CASSSSGDRPQGRSDPLEGFNRTMFNFNFNVVDPYVLRPVAVAWRDYVPQPARNGLSNFTSNLEEPAVMVNYFLQGDPYKGMVHFTRFFLNTILGMGGLIDVAGMANPQLQRVEPHRFGSTLGHYGVGYGPYVQLPFYGSFTLRDEGGDMADGLYPVLSWLTWPMSIGKWAVEGIETRAQLLDSDGLLRQSSDPYILMREAYFQRHDFIANGGKLTPADNPNAQAIQDELKDIDSQ

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

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	19

Entity 4 Entity 4 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	3

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5nupa_
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	d5nupb_
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	d5nupc_
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	5nupA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5nupB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5nupC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

▶

8. Citations (1)

▶

Unit-cell length a length_a	92.377 Å
Unit-cell length b length_b	145.240 Å
Unit-cell length c length_c	232.535 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	2.900 Å
Low-resolution limit resolution_low	68.383 Å
R factor r_factor	0.2432
R_work r_work	0.2408
R_free r_free	0.2905

fit	/app/data/saxs_computation/nu/5nup/5nup.fit
pddf	/app/data/pr_computation/nu/5nup/5nup.pr.out
profile	/app/data/saxs_computation/nu/5nup/5nup.dat

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

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

ABC transporter permease

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)