6rd3

Crystal structure of the wild type OmpK36 from Klebsiella pneumonia

Method: X-RAY DIFFRACTION D_max: 150.5 Å Quality: REASONABLE

▼

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	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
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 22–365 Chain E； UniProt 22–365 Chain F； UniProt 22–365	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

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 6RD3	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 mutation/modification 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
5O79 Klebsiella pneumoniae OmpK36 Deposited 2017-06-08	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）	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
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 mutation/modification 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 7 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 2–345； UniProt 22–365 Author chain B； PDBConstruct 2–345； UniProt 22–365 Author chain C； PDBConstruct 2–345； UniProt 22–365 Author chain D； PDBConstruct 2–345； UniProt 22–365 Author chain E； PDBConstruct 2–345； UniProt 22–365 Author chain F； PDBConstruct 2–345； 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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6rd3
Deposition date deposition_date	2019-04-12
Structure title title	Crystal structure of the wild type OmpK36 from Klebsiella pneumonia
Keywords keywords	OmpK36 WT, 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	48.04 Å
Radius of gyration Rg (electron density) rg_electron	48.98 Å
Forward intensity I(0) i0	819546000.00
Molecular weight molecular_weight	231540.0 kDa
Excluded volume excluded_volume	286360 Å³
Envelope volume envelope_volume	396360 Å³
Hydration-shell volume shell_volume	69139 Å³
Envelope diameter envelope_diameter	162.1 Å
Shell Rg shell_rg	50.38 Å
Envelope Rg envelope_rg	48.52 Å
Shape Rg shape_rg	48.98 Å
Total Rg total_rg	49.04 Å
Total atoms total_atoms	16401
Residues n_residues	2064
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	150.5 Å
Rg (real space) rg_real	49.34 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	8.0900e+08
I(0) uncertainty (real space) i0_real_error	1.2330e+07
Rg (reciprocal space) rg_reciprocal	48.05 Å
I(0) (reciprocal space) i0_reciprocal	819100000.0000
Solution quality estimate total_estimate	0.6441
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.440
Kurtosis Kurtosis kurtosis	-0.641
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	2.2680
Highest regularization parameter α highest_alpha	91880000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 0.935; Sysdev: 0.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.038

▶

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	38058.9 kDa
Mutation mutation	G0
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17283

GAEIYNKDGNKLDLYGKIDGLHYFSDDKSVDGDQTYMRVGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEGATNNGRGWSKQNGDGFGTSLTYDIWDGISAGFAYSHSKRTDEQNSVPALGRGDNAETYTGGLKYDANNIYLASQYTQTYNATRAGSLGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLERGYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNSFTRNAGISTDDVVALGLVYQF

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 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 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	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	882

▼

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6rd3a1
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	d6rd3a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6rd3b1
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	d6rd3b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6rd3c1
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	d6rd3c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6rd3d1
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	d6rd3d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6rd3e1
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	d6rd3e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6rd3f1
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	d6rd3f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	6rd3A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	6rd3B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	6rd3C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	6rd3D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	6rd3E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	6rd3F00
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	55.090 Å
Unit-cell length b length_b	316.090 Å
Unit-cell length c length_c	73.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	53.197 Å
R factor r_factor	0.1957
R_work r_work	0.1937
R_free r_free	0.2344

fit	/app/data/saxs_computation/rd/6rd3/6rd3.fit
pddf	/app/data/pr_computation/rd/6rd3/6rd3.pr.out
profile	/app/data/saxs_computation/rd/6rd3/6rd3.dat