SAXSdb — 9kn3

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

LPS-assembly protein LptD

Escherichia coli K-12

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–784	Not recorded	LPS-assembly lipoprotein LptE × 1 （P0ADC1） Uncharacterized lipoprotein YifL × 1 （P0ADN6）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.27 Å

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 9KN3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 203–784（582 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 203–784（582 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
9FZ5 Cryo-EM structure of LptDE-YedD complex from Escherichia Coli Deposited 2024-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–784（759 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Blot 3-4 seconds	Resolution 3.57 Å
9I9Z LpDE from Escherichia coli Deposited 2025-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9IA0 LpDE from Escherichia coli Deposited 2025-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9IA2 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9IA5 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9P1U beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly Deposited 2025-06-10	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9RPR Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM Deposited 2025-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–784（784 aa）	Not recorded	PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9Y0P Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I Deposited 2025-08-28	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 × 2 PDB declaration: dimeric	Chain B 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 NO3 NITRATE ION × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.210
9Y0P Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.210
9Y0Q Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode II Deposited 2025-08-28	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 × 2 PDB declaration: dimeric	Chain B 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.213

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPTD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–760； UniProt 25–784

LPS-assembly lipoprotein LptE

Escherichia coli K-12

UniProt P0ADC1

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 19–193	Not recorded	LPS-assembly protein LptD × 1 （P31554） Uncharacterized lipoprotein YifL × 1 （P0ADN6）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.27 Å

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 9KN3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NHR Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) Deposited 2013-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–182（163 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM Tris/HOAc pH 8.5, 200 mM KBr, 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.34 Å R-free 0.249
4NHR Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) Deposited 2013-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–182（163 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM Tris/HOAc pH 8.5, 200 mM KBr, 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.34 Å R-free 0.249
4RH8 Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–186（168 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.262
4RH8 Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–186（168 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.262
4RH8 Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 19–186（168 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.262
4RH8 Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 19–186（168 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.262
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–193（175 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 19–193（175 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
9FZ5 Cryo-EM structure of LptDE-YedD complex from Escherichia Coli Deposited 2024-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–167（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Blot 3-4 seconds	Resolution 3.57 Å
9I9Z LpDE from Escherichia coli Deposited 2025-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9IA0 LpDE from Escherichia coli Deposited 2025-02-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9IA2 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9IA5 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9P1U beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly Deposited 2025-06-10	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPTE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–175； UniProt 19–193

Uncharacterized lipoprotein YifL

Escherichia coli K-12

UniProt P0ADN6

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 20–67	Not recorded	LPS-assembly protein LptD × 1 （P31554） LPS-assembly lipoprotein LptE × 1 （P0ADC1）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.27 Å

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 9KN3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H1R Crystal structure of LptDE-YifL complex Deposited 2022-10-03	Different construct 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 1–67（67 aa）	Not recorded	PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；175 mM citric acid/Bis-Tris (pH 5.0), 17% (v/v) PEG3350 and 3% methanol (as additive)	Resolution 2.98 Å R-free 0.264
8H1R Crystal structure of LptDE-YifL complex Deposited 2022-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–67（67 aa）	Not recorded	PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；175 mM citric acid/Bis-Tris (pH 5.0), 17% (v/v) PEG3350 and 3% methanol (as additive)	Resolution 2.98 Å R-free 0.264
9IA2 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–67（67 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9IA5 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–67（67 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9RPR Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM Deposited 2025-06-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–67（48 aa）	Not recorded	PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9RPS Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM Deposited 2025-06-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 20–67（48 aa）	Not recorded	PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YIFL_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 20–67

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	9kn3
Deposition date deposition_date	2024-11-18
Structure title title	Cryo-EM structure of LptDEM complex from Escherichia coli
Keywords keywords	LPS, Transporter, Complex, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	34.57 Å
Radius of gyration Rg (electron density) rg_electron	34.19 Å
Forward intensity I(0) i0	182592000.00
Molecular weight molecular_weight	104760.0 kDa
Excluded volume excluded_volume	129500 Å³
Envelope volume envelope_volume	175810 Å³
Hydration-shell volume shell_volume	44435 Å³
Envelope diameter envelope_diameter	124.9 Å
Shell Rg shell_rg	39.77 Å
Envelope Rg envelope_rg	33.80 Å
Shape Rg shape_rg	34.21 Å
Total Rg total_rg	34.57 Å
Total atoms total_atoms	7392
Residues n_residues	917
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	117.2 Å
Rg (real space) rg_real	34.71 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	1.8260e+08
I(0) uncertainty (real space) i0_real_error	2.8510e+06
Rg (reciprocal space) rg_reciprocal	34.62 Å
I(0) (reciprocal space) i0_reciprocal	182600000.0000
Solution quality estimate total_estimate	0.6618
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.2 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.160
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21240000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.980; Smooth: 0.787

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LPS-assembly protein LptD
Molecular weight formula_weight	87149.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7392

ADLASQCMLGVPSYDRPLVQGDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGDKRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKLLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGISQVGAVASWPIADRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LPS-assembly lipoprotein LptE
Molecular weight formula_weight	19479.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

CGWHLRDTTQVPSTMKVMILDSGDPNGPLSRAVRNQLRLNGVELLDKETTRKDVPSLRLGKVSIAKDTASVFRNGQTAEYQMIMTVNATVLIPGRDIYPISAKVFRSFFDNPQMALAKDNEQDMIVKEMYDRAAEQLIRKLPSIRAADIRSDEEQTSTTTDTPATPARVSTTLGN

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Uncharacterized lipoprotein YifL
Molecular weight formula_weight	6727.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

CGLKGPLYFPPADKNAPPPTKPVETQTQSTVPDKNDRATGDGPSQVNYLEHHHHHHHHHH

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.27 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	428907

fit	/app/data/saxs_computation/kn/9kn3/9kn3.fit
pddf	/app/data/pr_computation/kn/9kn3/9kn3.pr.out
profile	/app/data/saxs_computation/kn/9kn3/9kn3.dat

Cryo-EM structure of LptDEM complex from Escherichia coli

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

LPS-assembly protein LptD

State in the Current Structure

Other States of the Same Protein in the Database

LPS-assembly lipoprotein LptE

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized lipoprotein YifL

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)