SAXSdb — 9lpl

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

3-oxoacyl-[acyl-carrier-protein] synthase 2

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–413 Chain B； UniProt 2–413	Mutation：C163Q	A1EWE 3-(3-((2S,3S,5S,5aR,6S,12cR)-11-(tert-butyl)-2,6-dimethyl-7-oxo-1,2,3,4,5,5a,6,7-octahydro-2,5-epoxy-3,12c-methanobenzo[b]cyclohepta[5,6]benzo[1,2-d]thiophen-6-yl)propanamido)-2,4-dihydroxybenzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M BIS-Tris, 0.2 M Magnesium chloride, 20 % w/v polyethylene glycol (PEG) 3350	Resolution 2.70 Å R-free 0.263

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 9LPL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B3N BETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICATIONS FROM THE CRYSTAL STRUCTURE OF A COMPLEX WITH THE INHIBITOR CERULENIN. Deposited 1998-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Not recorded	CER (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；5.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL WERE MIXED (2+2UL) WITH A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000 0.1% V/V 2-MERCAPTOETHANOL AND WATER. CRYSTALS APPEARED IN A FEW DAYS	Resolution 2.65 Å R-free 0.270
1KAS BETA-KETOACYL-ACP SYNTHASE II FROM ESCHERICHIA COLI Deposited 1997-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–412（412 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.279
2GFV Structure of E. coli FabF (KASII) C163Q mutant Deposited 2006-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–412（412 aa）	Mutation：C163Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.29 Å R-free 0.247
2GFW Structure of wild type E. coli FabF (KASII) Deposited 2006-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–412（412 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.268
2GFX Structure of E. coli FabF(C163Q) in complex with Platensimycin Deposited 2006-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–412（412 aa）	Mutation：C163Q	PMN PLATENSIMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.59 Å R-free 0.255
2GFY Structure of E. coli FabF(K335A) mutant with covalently linked dodecanoic acid Deposited 2006-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–412（412 aa）	Mutation：K335A	DAO LAURIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.243
3G0Y Structure of E. coli FabF(C163Q) in complex with dihydroplatensimycin Deposited 2009-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Mutation：C163Q	P9A 3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxodecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.234
3G11 Structure of E. coli FabF(C163Q) in complex with dihydrophenyl platensimycin Deposited 2009-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Mutation：C163Q	P9C 3-({3-[(1S,4S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxo-4-phenyldecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.204
3HNZ Structure of E. coli FabF(C163A) in Complex with Platensimycin Deposited 2009-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Mutation：C163A	PMN PLATENSIMYCIN × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.75 Å R-free 0.256
3HO2 Structure of E.coli FabF(C163A) in complex with Platencin Deposited 2009-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Mutation：C163A	N32 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.207
3HO9 Structure of E.coli FabF(C163A) in complex with Platencin A1 Deposited 2009-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–413（412 aa）	Mutation：C163A	N3A 2,4-dihydroxy-3-({3-[(2R,4aR,8S,8aR,9R)-9-hydroxy-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonap hthalen-8-yl]propanoyl}amino)benzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.90 Å R-free 0.190
3I8P Crystal structure of E. coli FabF(C163A) in complex with Platensimycin A1 Deposited 2009-07-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–413（413 aa）	Mutation：C163A	840 Platensimycin A1 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；19-24% PEG 8000, 0.1M Tris-HCl, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.182
6OKG Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16-crypto Acyl Carrier Protein, AcpP Deposited 2019-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–413（413 aa）	Not recorded	NA SODIUM ION × 2 MU4 N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate	Resolution 2.30 Å R-free 0.228
6OLT Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C12-crypto Acyl Carrier Protein, AcpP Deposited 2019-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–413（413 aa）	Not recorded	MRJ N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate	Resolution 2.35 Å R-free 0.239
7L4E Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16:1-crypto Acyl Carrier Protein, AcpP Deposited 2020-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–413（413 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 MU4 N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate	Resolution 2.00 Å R-free 0.207
7L4L Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C8-crypto Acyl Carrier Protein, AcpP Deposited 2020-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–413（413 aa） Chain B 1–413（413 aa）	Not recorded	NA SODIUM ION × 2 DYF [(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate	Resolution 2.65 Å R-free 0.267

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FABF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–430； UniProt 2–413 Author chain B； PDBConstruct 19–430； UniProt 2–413

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	9lpl
Deposition date deposition_date	2025-01-25
最后修订 last_revision	2026-01-28
Structure title title	E. coli FabF mutant -C163Q
Keywords keywords	Complex, Inhibitor, TRANSFERASE; TRANSFERASE
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	26.09 Å
Radius of gyration Rg (electron density) rg_electron	25.19 Å
Forward intensity I(0) i0	236732000.00
Molecular weight molecular_weight	80470.0 kDa
Excluded volume excluded_volume	77028 Å³
Envelope volume envelope_volume	121610 Å³
Hydration-shell volume shell_volume	38054 Å³
Envelope diameter envelope_diameter	85.9 Å
Shell Rg shell_rg	34.32 Å
Envelope Rg envelope_rg	25.48 Å
Shape Rg shape_rg	25.17 Å
Total Rg total_rg	25.84 Å
Total atoms total_atoms	6075
Residues n_residues	819
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	80.9 Å
Rg (real space) rg_real	25.95 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.3670e+08
I(0) uncertainty (real space) i0_real_error	3.0380e+06
Rg (reciprocal space) rg_reciprocal	25.99 Å
I(0) (reciprocal space) i0_reciprocal	236700000.0000
Solution quality estimate total_estimate	0.8227
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.219
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60590000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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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	3-oxoacyl-[acyl-carrier-protein] synthase 2
Molecular weight formula_weight	46549.4 kDa
EC 编号 ec_number	2.3.1.179
Mutation mutation	C163Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6120

HHHHHHSSGLVPRGSHMVSKRRVVVTGLGMLSPVGNTVESTWKALLAGQSGISLIDHFDTSAYATKFAGLVKDFNCEDIISRKEQRKMDAFIQYGIVAGVQAMQDSGLEITEENATRIGAAIGSGIGGLGLIEENHTSLMNGGPRKISPFFVPSTIVNMVAGHLTIMYGLRGPSISIATAQTSGVHNIGHAARIIAYGDADVMVAGGAEKASTPLGVGGFGAARALSTRNDNPQAASRPWDKERDGFVLGDGAGMLVLEEYEHAKKRGAKIYAELVGFGMSSDAYHMTSPPENGAGAALAMANALRDAGIEASQIGYVNAHGTSTPAGDKAEAQAVKTIFGEAASRVLVSSTKSMTGHLLGAAGAVESIYSILALRDQAVPPTINLDNPDEGCDLDFVPHEARQVSGMEYTLCNSFGFGGTNGSLIFKKIKLAAALEHHHHHH

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;3-(3-((2S,3S,5S,5aR,6S,12cR)-11-(tert-butyl)-2,6-dimethyl-7-oxo-1,2,3,4,5,5a,6,7-octahydro-2,5-epoxy-3,12c-methanobenzo[b]cyclohepta[5,6]benzo[1,2-d]thiophen-6-yl)propanamido)-2,4-dihydroxybenzoic acid ;
Molecular weight formula_weight	603.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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8. Citations (1)

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Unit-cell length a length_a	79.761 Å
Unit-cell length b length_b	79.761 Å
Unit-cell length c length_c	299.191 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	33.270 Å
R factor r_factor	0.2067
R_work r_work	0.2038
R_free r_free	0.2630

fit	/app/data/saxs_computation/lp/9lpl/9lpl.fit
pddf	/app/data/pr_computation/lp/9lpl/9lpl.pr.out
profile	/app/data/saxs_computation/lp/9lpl/9lpl.dat

E. coli FabF mutant -C163Q

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

3-oxoacyl-[acyl-carrier-protein] synthase 2

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