SAXSdb — 6f49

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

Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 48–179 Chain A； UniProt 180–266	Mutation：delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M ammonium sulfate, 0.15 M sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 2.02 Å R-free 0.233
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 48–179 Chain B； UniProt 180–266	Mutation：delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A	GOL GLYCEROL × 3 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M ammonium sulfate, 0.15 M sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 2.02 Å R-free 0.233
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 48–179 Chain C； UniProt 180–266	Mutation：delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A	GOL GLYCEROL × 3 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M ammonium sulfate, 0.15 M sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 2.02 Å R-free 0.233
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 48–179 Chain D； UniProt 180–266	Mutation：delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M ammonium sulfate, 0.15 M sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 2.02 Å R-free 0.233

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 6F49	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NAA Lipoprotein-releasing system transmembrane protein LolC Deposited 2017-02-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–266（219 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 1.88 Å R-free 0.225
5NAA Lipoprotein-releasing system transmembrane protein LolC Deposited 2017-02-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 48–266（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288.15 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6, 30% w/v PEG 2000 MME	Resolution 1.88 Å R-free 0.225
6F3Z Complex of E. coli LolA and periplasmic domain of LolC Deposited 2017-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 48–266（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288.15 K；45% w/v Poly(acrylic acid sodium salt) 2100, 100 mM HEPES pH 6.5	Resolution 2.00 Å R-free 0.249
6F3Z Complex of E. coli LolA and periplasmic domain of LolC Deposited 2017-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 48–266（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288.15 K；45% w/v Poly(acrylic acid sodium salt) 2100, 100 mM HEPES pH 6.5	Resolution 2.00 Å R-free 0.249
7MDX LolCDE nucleotide-free Deposited 2021-04-06	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 A 2–394（393 aa）	Not recorded	F15 PENTADECANOIC ACID × 1 ZM5 (2R)-2-(tridecanoyloxy)propyl hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7V8I LolCD(E171Q)E with bound AMPPNP in nanodiscs Deposited 2021-08-23	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 × 4 PDB declaration: tetrameric	Chain C 1–399（399 aa）	Not recorded	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.60 Å
7V8L LolCDE with bound RcsF in nanodiscs Deposited 2021-08-23	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 C 1–399（399 aa）	Not recorded	PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.50 Å
7V8M LolCDE-apo in nanodiscs Deposited 2021-08-23	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 × 4 PDB declaration: tetrameric	Chain C 1–399（399 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.20 Å
9GRC Cryo-EM structure of lipoprotein-bound LolCDE in nanodiscs Deposited 2024-09-11	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 C 1–399（399 aa）	Not recorded	Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9GVK Cryo-EM structure of endogenous ATP-bound LolCDE with LolD-E171Q mutations in nanodiscs Deposited 2024-09-25	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 × 4 PDB declaration: tetrameric	Chain C 1–399（399 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
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 C 1–399（399 aa）	Not recorded	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 C 1–399（399 aa）	Not recorded	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
9RLE LolCDE complex with Pal 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 C 1–399（399 aa）	Not recorded	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 3.18 Å
9RLF LolCDE complex with Pal 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 C 1–399（399 aa）	Not recorded	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 3.17 Å
9RLG LolCDE complex with LolB 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 C 1–399（399 aa）	Not recorded	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 3.09 Å
9RLH LolCDE complex with del 9-15 LolB 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 C 1–399（399 aa）	Not recorded	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 3.19 Å
9RLI LolCDEdelta(235-252) complex with Pal 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 C 1–399（399 aa）	Not recorded	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 3.63 Å
9RLJ LolCDE with bound ATPgammaS 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 × 4 PDB declaration: tetrameric	Chain C 1–399（399 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9RLK LolCDE(delta 235-252) complex with Pal 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 C 1–399（399 aa）	Not recorded	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 3.29 Å
9XRO LolCDE in complex with SMT-738_3 Deposited 2025-11-19	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 × 3 PDB declaration: trimeric	Chain C 1–399（399 aa）	Not recorded	A1ER4 2-azanyl-1-[6-[2-azanyl-5-(3-methylpyridin-4-yl)-1H-imidazol-4-yl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methyl-propan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å

18 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LOLC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 48–179 Author chain A； PDBConstruct 122–208； UniProt 180–266 Author chain B； PDBConstruct 1–121； UniProt 48–179 Author chain B； PDBConstruct 122–208； UniProt 180–266 Author chain C； PDBConstruct 1–121； UniProt 48–179 Author chain C； PDBConstruct 122–208； UniProt 180–266 Author chain D； PDBConstruct 1–121； UniProt 48–179 Author chain D； PDBConstruct 122–208； UniProt 180–266

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	6f49
Deposition date deposition_date	2017-11-29
Structure title title	Periplasmic domain of LolC lacking the Hook.
Keywords keywords	lipoprotein trafficking, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	35.62 Å
Radius of gyration Rg (electron density) rg_electron	35.58 Å
Forward intensity I(0) i0	139572000.00
Molecular weight molecular_weight	94211.0 kDa
Excluded volume excluded_volume	117780 Å³
Envelope volume envelope_volume	149630 Å³
Hydration-shell volume shell_volume	37018 Å³
Envelope diameter envelope_diameter	123.6 Å
Shell Rg shell_rg	39.42 Å
Envelope Rg envelope_rg	35.57 Å
Shape Rg shape_rg	35.58 Å
Total Rg total_rg	35.85 Å
Total atoms total_atoms	6611
Residues n_residues	841
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	121.8 Å
Rg (real space) rg_real	35.91 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	1.3960e+08
I(0) uncertainty (real space) i0_real_error	2.4850e+06
Rg (reciprocal space) rg_reciprocal	35.74 Å
I(0) (reciprocal space) i0_reciprocal	139500000.0000
Solution quality estimate total_estimate	0.7725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.512
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17730000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.783; Smooth: 0.000

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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	Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
Molecular weight formula_weight	24379.7 kDa
Mutation mutation	delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7175

MNGFERELQNNILGLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPAQKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVGASQRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKLPEGSKWQDWRDRKGELFQAVRMEKNMAAALEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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8. Citations (1)

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Unit-cell length a length_a	75.310 Å
Unit-cell length b length_b	108.540 Å
Unit-cell length c length_c	109.450 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.020 Å
Low-resolution limit resolution_low	62.040 Å
R factor r_factor	0.1906
R_work r_work	0.1884
R_free r_free	0.2328

fit	/app/data/saxs_computation/f4/6f49/6f49.fit
pddf	/app/data/pr_computation/f4/6f49/6f49.pr.out
profile	/app/data/saxs_computation/f4/6f49/6f49.dat

Periplasmic domain of LolC lacking the Hook.

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

Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC

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