SAXSdb — 1kfm

▼

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

MAJOR OUTER MEMBRANE LIPOPROTEIN

Escherichia coli

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 22–77	Mutation：M30A, V34A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；PEG 4000, sodium cacodylate, ammonium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.288

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 1KFM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EQ7 CORE STRUCTURE OF THE OUTER MEMBRANE LIPOPROTEIN FROM ESCHERICHIA COLI AT 1.9 ANGSTROM RESOLUTION Deposited 2000-04-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–77（56 aa） Fragment：PROTEIN MOIETY	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 4000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.269
1JCC Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations Deposited 2001-06-08	Different construct 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 22–77（56 aa） Chain B 22–77（56 aa） Chain C 22–77（56 aa）	Mutation：V13A,L16A,V20A,L23A,V27A,M30A,V34A Mutation：V13A,L16A,V20A,L23A,V27A,M30A,V34A Mutation：V13A,L16A,V20A,L23A,V27A,M30A,V34A	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；Sodium acetate, zinc acetate, PEG 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.223
1JCD Crystal Structure of a Novel Alanine-Zipper Trimer at 1.3 A Resolution, I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A mutations Deposited 2001-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–73（52 aa） Chain B 22–73（52 aa） Chain C 22–73（52 aa）	Mutation：I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A Mutation：I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A Mutation：I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；Sodium acetate, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.30 Å R-free 0.209
1KFN Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants Deposited 2001-11-21	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–77（56 aa）	Mutation：L23A, V27A, M30A, V34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；PEG 4000, sodium acetate, ammonium acetate, L-cystein, pH 4.0, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.272
1T8Z Atomic Structure of A Novel Tryptophan-Zipper Pentamer Deposited 2004-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 22–74（53 aa） Chain B 22–74（53 aa） Chain C 22–74（53 aa） Chain D 22–74（53 aa） Chain E 22–74（53 aa）	Mutation：I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W Mutation：I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W Mutation：I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W Mutation：I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W Mutation：I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W	SO4 SULFATE ION × 2 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, Tris-HCl, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.45 Å R-free 0.277
2GUS Conformational Transition between Four- and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction Deposited 2006-05-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 22–77（56 aa）	Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27M, M30F, V34F, A37F, A41F, A44F, L48F, M51F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1M Tris-HCl, 10mM nickel chloride, 14% PEG MME2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.75 Å R-free 0.287
2GUV Conformational Transition between Four- and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction Deposited 2006-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 22–77（56 aa） Chain B 22–77（56 aa） Chain C 22–77（56 aa） Chain D 22–77（56 aa） Chain E 22–77（56 aa）	Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27F, M30F, V34F, A37F, A41F, A44F, L48F, M51F Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27F, M30F, V34F, A37F, A41F, A44F, L48F, M51F Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27F, M30F, V34F, A37F, A41F, A44F, L48F, M51F Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27F, M30F, V34F, A37F, A41F, A44F, L48F, M51F Mutation：I6F, L9F, V13F, L16F, V20F, L23F, V27F, M30F, V34F, A37F, A41F, A44F, L48F, M51F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1M Tris-HCl, 15% isopropanol, 1,4-butanediol, 23% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.252
9RLC LolCDE complex with Lpp lipoprotein Deposited 2025-06-16	Different construct 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 × 5 PDB declaration: pentameric	Chain L 21–77（57 aa）	Mutation：delta K58 and C-terminal linker-strep II tag LESAWSHPQFEK	PLM PALMITIC ACID × 1 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9RLD LolCDE complex with Lpp lipoprotein Deposited 2025-06-16	Different construct 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 × 5 PDB declaration: pentameric	Chain L 21–77（57 aa）	Mutation：DeltaK58 and linker-strep II tag (LESAWSHPQF)EK	PLM PALMITIC ACID × 1 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 22–77

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	1kfm
Deposition date deposition_date	2001-11-21
Structure title title	Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants
Keywords keywords	LIPOPROTEIN, PROTEIN FOLDING, HELIX CAPPING, ALANINE-ZIPPER, 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	20.81 Å
Radius of gyration Rg (electron density) rg_electron	21.86 Å
Forward intensity I(0) i0	744400.00
Molecular weight molecular_weight	5194.0 kDa
Excluded volume excluded_volume	6231 Å³
Envelope volume envelope_volume	9267 Å³
Hydration-shell volume shell_volume	5031 Å³
Envelope diameter envelope_diameter	78.6 Å
Shell Rg shell_rg	22.02 Å
Envelope Rg envelope_rg	22.69 Å
Shape Rg shape_rg	21.79 Å
Total Rg total_rg	22.07 Å
Total atoms total_atoms	363
Residues n_residues	50
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	81.4 Å
Rg (real space) rg_real	21.56 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	7.4440e+05
I(0) uncertainty (real space) i0_real_error	1.0980e+04
Rg (reciprocal space) rg_reciprocal	21.42 Å
I(0) (reciprocal space) i0_reciprocal	744300.0000
Solution quality estimate total_estimate	0.6196
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	9.4 Å
Skewness Skewness skewness	0.683
Kurtosis Kurtosis kurtosis	-0.324
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23650.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.034; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.004; Smooth: 0.946

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kfma_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.16 — Outer membrane lipoprotein
Family Family family	h.1.16.1 — Outer membrane lipoprotein

CATH v4.4 (1 domains)

Domain ID domain_id	1kfmA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	190 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	37.057 Å
Unit-cell length b length_b	37.057 Å
Unit-cell length c length_c	81.912 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.260 Å
R factor r_factor	0.2600
R_work r_work	0.2600
R_free r_free	0.2880

Description description	MAJOR OUTER MEMBRANE LIPOPROTEIN
Molecular weight formula_weight	6073.6 kDa
Mutation mutation	M30A, V34A
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	382

Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants

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

MAJOR OUTER MEMBRANE LIPOPROTEIN

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

fit	/app/data/saxs_computation/kf/1kfm/1kfm.fit
pddf	/app/data/pr_computation/kf/1kfm/1kfm.pr.out
profile	/app/data/saxs_computation/kf/1kfm/1kfm.dat