SAXSdb — 7pzf

▼

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：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
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：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

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 7PZF	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
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
7Q3T Crystal structure of the OmpK36 D insertion chimera from Klebsiella pneumonia Deposited 2021-10-28	Different mutation/modification Different ligand/ion 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 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 2–347； UniProt 22–365 Author chain B； PDBConstruct 2–347； UniProt 22–365 Author chain C； PDBConstruct 2–347； UniProt 22–365 Author chain D； PDBConstruct 2–347； UniProt 22–365 Author chain E； PDBConstruct 2–347； UniProt 22–365 Author chain F； PDBConstruct 2–347； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7pzf
Deposition date deposition_date	2021-10-12
Structure title title	Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia
Keywords keywords	outer membrane porin, 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	49.55 Å
Radius of gyration Rg (electron density) rg_electron	50.38 Å
Forward intensity I(0) i0	807844000.00
Molecular weight molecular_weight	232360.0 kDa
Excluded volume excluded_volume	288190 Å³
Envelope volume envelope_volume	399000 Å³
Hydration-shell volume shell_volume	67185 Å³
Envelope diameter envelope_diameter	165.8 Å
Shell Rg shell_rg	51.79 Å
Envelope Rg envelope_rg	49.69 Å
Shape Rg shape_rg	50.37 Å
Total Rg total_rg	50.45 Å
Total atoms total_atoms	16475
Residues n_residues	2078
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	154.8 Å
Rg (real space) rg_real	50.03 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	8.0780e+08
I(0) uncertainty (real space) i0_real_error	1.4660e+07
Rg (reciprocal space) rg_reciprocal	49.55 Å
I(0) (reciprocal space) i0_reciprocal	807300000.0000
Solution quality estimate total_estimate	0.5749
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.431
Kurtosis Kurtosis kurtosis	-0.665
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	71500000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.907; Smooth: 0.008

▶

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	38275.1 kDa
Mutation mutation	T115 and D116 insertion
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	17802

GAEIYNKDGNKLDLYGKIDGLHYFSDDKSVDGDQTYMRVGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEGATNNGRGWSKQNGDGFGTSLTYDIWDGISAGFAYSHSKRTDEQNSVPALGRGDNAETYTGGLKYDANNIYLASQYTQTYNATRAGSLGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLERGYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNSFTRNAGISTDDVVALGLVYQF

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	LITHIUM ION
Molecular weight formula_weight	6.9 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	TETRADECANE
Molecular weight formula_weight	198.4 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1206

▶

8. Citations (1)

▶

Unit-cell length a length_a	55.106 Å
Unit-cell length b length_b	73.428 Å
Unit-cell length c length_c	158.837 Å
Unit-cell angle α angle_alpha	91.12 °
Unit-cell angle β angle_beta	97.17 °
Unit-cell angle γ angle_gamma	103.09 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.499 Å
Low-resolution limit resolution_low	54.250 Å
R factor r_factor	0.1909
R_work r_work	0.1901
R_free r_free	0.2053

fit	/app/data/saxs_computation/pz/7pzf/7pzf.fit
pddf	/app/data/pr_computation/pz/7pzf/7pzf.pr.out
profile	/app/data/saxs_computation/pz/7pzf/7pzf.dat

Crystal structure of the OmpK36 TD insertion chimera from Klebsiella pneumonia

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