SAXSdb — 2gfx

▼

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

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

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–412	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

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 2GFX	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 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 ligand/ion 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 mutation/modification Different ligand/ion 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
2GFY Structure of E. coli FabF(K335A) mutant with covalently linked dodecanoic acid Deposited 2006-03-23	Different mutation/modification Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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
9LPL E. coli FabF mutant -C163Q Deposited 2025-01-25	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） Chain B 2–413（412 aa）	Mutation：C163Q 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

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 16–427； UniProt 1–412

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	2gfx
Deposition date deposition_date	2006-03-23
Structure title title	Structure of E. coli FabF(C163Q) in complex with Platensimycin
Keywords keywords	FabF; KASII; ketoacyl synthase; platensimycin, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.52 Å
Radius of gyration Rg (electron density) rg_electron	20.43 Å
Forward intensity I(0) i0	32712800.00
Molecular weight molecular_weight	43286.0 kDa
Excluded volume excluded_volume	53823 Å³
Envelope volume envelope_volume	60606 Å³
Hydration-shell volume shell_volume	24140 Å³
Envelope diameter envelope_diameter	75.7 Å
Shell Rg shell_rg	27.87 Å
Envelope Rg envelope_rg	20.93 Å
Shape Rg shape_rg	20.42 Å
Total Rg total_rg	21.33 Å
Total atoms total_atoms	3040
Residues n_residues	411
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	74.2 Å
Rg (real space) rg_real	21.42 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	3.2710e+07
I(0) uncertainty (real space) i0_real_error	4.3950e+05
Rg (reciprocal space) rg_reciprocal	21.44 Å
I(0) (reciprocal space) i0_reciprocal	32710000.0000
Solution quality estimate total_estimate	0.8650
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8449000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.994

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

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	44662.3 kDa
EC 编号 ec_number	2.3.1.41
Mutation mutation	C163Q
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	3150

MRGSHHHHHHGSACVSKRRVVVTGLGMLSPVGNTVESTWKALLAGQSGISLIDHFDTSAYATKFAGLVKDFNCEDIISRKEQRKMDAFIQYGIVAGVQAMQDSGLEITEENATRIGAAIGSGIGGLGLIEENHTSLMNGGPRKISPFFVPSTIVNMVAGHLTIMYGLRGPSISIATAQTSGVHNIGHAARIIAYGDADVMVAGGAEKASTPLGVGGFGAARALSTRNDNPQAASRPWDKERDGFVLGDGAGMLVLEEYEHAKKRGAKIYAELVGFGMSSDAYHMTSPPENGAGAALAMANALRDAGIEASQIGYVNAHGTSTPAGDKAEAQAVKTIFGEAASRVLVSSTKSMTGHLLGAAGAVESIYSILALRDQAVPPTINLDNPDEGCDLDFVPHEARQVSGMEYTLCNSFGFGGTNGSLIFKKI

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	PLATENSIMYCIN
Molecular weight formula_weight	441.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2gfxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.1 — Thiolase-related

Domain ID domain_id	d2gfxa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.1 — Thiolase-related

CATH v4.4 (2 domains)

Domain ID domain_id	2gfxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	2gfxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

▶

8. Citations (1)

▶

Unit-cell length a length_a	75.727 Å
Unit-cell length b length_b	75.727 Å
Unit-cell length c length_c	147.304 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	65.940 Å
R factor r_factor	0.1971
R_work r_work	0.1942
R_free r_free	0.2553

fit	/app/data/saxs_computation/gf/2gfx/2gfx.fit
pddf	/app/data/pr_computation/gf/2gfx/2gfx.pr.out
profile	/app/data/saxs_computation/gf/2gfx/2gfx.dat

Structure of E. coli FabF(C163Q) in complex with Platensimycin

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