2vb9

beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure

Method: X-RAY DIFFRACTION D_max: 128.7 Å Quality: GOOD

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

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

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 1–406 Chain B； UniProt 1–406	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5	Resolution 1.50 Å R-free 0.238
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–406 Chain D； UniProt 1–406	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5	Resolution 1.50 Å R-free 0.238

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 2VB9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DD8 CRYSTAL STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I FROM ESCHERICHIA COLI Deposited 1999-11-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；bis-tris propane, ammonium sulfate, PEG400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 2.30 Å R-free 0.219
1DD8 CRYSTAL STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I FROM ESCHERICHIA COLI Deposited 1999-11-09	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；bis-tris propane, ammonium sulfate, PEG400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 2.30 Å R-free 0.219
1EK4 BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH DODECANOIC ACID TO 1.85 RESOLUTION Deposited 2000-03-06	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 1–406（406 aa） Chain B 1–406（406 aa）	Mutation：C163S, MRGSHHHHHHGS N-TERMINAL HIS-TAG (NOT IN MODEL) Mutation：C163S, MRGSHHHHHHGS N-TERMINAL HIS-TAG (NOT IN MODEL)	DAO LAURIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；1.8 M ammonium sulfate, 2 % PEG400, 0.1 M bis-Tris propane, pH 6.5, resulting pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.196
1EK4 BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH DODECANOIC ACID TO 1.85 RESOLUTION Deposited 2000-03-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Mutation：C163S, MRGSHHHHHHGS N-TERMINAL HIS-TAG (NOT IN MODEL) Mutation：C163S, MRGSHHHHHHGS N-TERMINAL HIS-TAG (NOT IN MODEL)	DAO LAURIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；1.8 M ammonium sulfate, 2 % PEG400, 0.1 M bis-Tris propane, pH 6.5, resulting pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.196
1F91 BETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I IN COMPLEX WITH C10 FATTY ACID SUBSTRATE Deposited 2000-07-06	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 1–406（406 aa） Chain B 1–406（406 aa）	Mutation：C163S Mutation：C163S	OH HYDROXIDE ION × 2 DKA DECANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；294 K；1.9 M ammonium sulfate, 2% PEG400, 0.1 M bis-Tris propane pH 6.5, pH 7.4, VAPOR DIFFUSION, temperature 294K	Resolution 2.40 Å R-free 0.209
1F91 BETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I IN COMPLEX WITH C10 FATTY ACID SUBSTRATE Deposited 2000-07-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Mutation：C163S Mutation：C163S	OH HYDROXIDE ION × 2 DKA DECANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；294 K；1.9 M ammonium sulfate, 2% PEG400, 0.1 M bis-Tris propane pH 6.5, pH 7.4, VAPOR DIFFUSION, temperature 294K	Resolution 2.40 Å R-free 0.209
1FJ4 THE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH THIOLACTOMYCIN, IMPLICATIONS FOR DRUG DESIGN Deposited 2000-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	TLM THIOLACTOMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Ammonium Sulfate, PEG 400, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.35 Å R-free 0.253
1FJ4 THE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH THIOLACTOMYCIN, IMPLICATIONS FOR DRUG DESIGN Deposited 2000-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	TLM THIOLACTOMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Ammonium Sulfate, PEG 400, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.35 Å R-free 0.253
1FJ8 THE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH CERULENIN, IMPLICATIONS FOR DRUG DESIGN Deposited 2000-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	CER (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；ammonium sulfate, PEG 400, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.27 Å R-free 0.265
1FJ8 THE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH CERULENIN, IMPLICATIONS FOR DRUG DESIGN Deposited 2000-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	CER (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；ammonium sulfate, PEG 400, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.27 Å R-free 0.265
1G5X The Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase I Deposited 2000-11-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；ammonium sulfate, PEG 400, tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.45 Å R-free 0.266
1G5X The Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase I Deposited 2000-11-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；ammonium sulfate, PEG 400, tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.45 Å R-free 0.266
2AQ7 Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli Deposited 2005-08-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	TL5 (5R)-4-HYDROXY-3,5-DIMETHYL-5-[(1E,3E)-2-METHYLPENTA-1,3-DIENYL]THIOPHEN-2(5H)-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.228
2AQ7 Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli Deposited 2005-08-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	TL5 (5R)-4-HYDROXY-3,5-DIMETHYL-5-[(1E,3E)-2-METHYLPENTA-1,3-DIENYL]THIOPHEN-2(5H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.228
2AQB Structure-activity relationships at the 5-position of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherchia coli Deposited 2005-08-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	TL6 (5R)-5-[(1E)-BUTA-1,3-DIENYL]-4-HYDROXY-3,5-DIMETHYLTHIOPHEN-2(5H)-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.19 Å R-free 0.225
2AQB Structure-activity relationships at the 5-position of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherchia coli Deposited 2005-08-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	TL6 (5R)-5-[(1E)-BUTA-1,3-DIENYL]-4-HYDROXY-3,5-DIMETHYLTHIOPHEN-2(5H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.19 Å R-free 0.225
2VB7 beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure after soak in PEG solution Deposited 2007-09-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5 SOAK IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, NO LIGAND	Resolution 1.60 Å R-free 0.186
2VB7 beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure after soak in PEG solution Deposited 2007-09-06	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5 SOAK IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, NO LIGAND	Resolution 1.60 Å R-free 0.186
2VB8 beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin Deposited 2007-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	TLM THIOLACTOMYCIN × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5; SOAK WITH 0.3MM LIGAND IN 2.3M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 3% DMSO	Resolution 1.52 Å R-free 0.185
2VB8 beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin Deposited 2007-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	TLM THIOLACTOMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5; SOAK WITH 0.3MM LIGAND IN 2.3M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 3% DMSO	Resolution 1.52 Å R-free 0.185
2VBA beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor Deposited 2007-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	P4T 2-PHENYLAMINO-4-METHYL-5-ACETYL THIAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5 SOAK WITH 0.01M LIGAND IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 0.005M TCEP	Resolution 1.36 Å R-free 0.151
2VBA beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor Deposited 2007-09-06	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–406（406 aa） Chain D 1–406（406 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5 SOAK WITH 0.01M LIGAND IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 0.005M TCEP	Resolution 1.36 Å R-free 0.151
6OKC Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C12-crypto Acyl Carrier Protein, AcpP Deposited 2019-04-12	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 1–406（406 aa） Chain B 1–406（406 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；20% PEG 8K, 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5	Resolution 1.55 Å R-free 0.164
6OKF Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16-crypto Acyl Carrier Protein, AcpP Deposited 2019-04-12	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 1–406（406 aa） Chain B 1–406（406 aa）	Not recorded	NA SODIUM ION × 2 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；26% PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate	Resolution 2.50 Å R-free 0.218
7SZ9 Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16:1-crypto Acyl Carrier Protein, AcpP Deposited 2021-11-26	Different construct 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 2–405（404 aa） Chain B 2–405（404 aa）	Not recorded	NA SODIUM ION × 2 DJ5 N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-{[(9Z)-hexadec-9-enoyl]amino}ethyl)-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；20% PEG 8000, 0.3 M sodium acetate, 0.1 M sodium cacodylate	Resolution 2.20 Å R-free 0.255
8SMS Crosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin crosslinker-crypto Acyl Carrier Protein, AcpP Deposited 2023-04-26	Different construct 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 2–405（404 aa） Chain B 2–405（404 aa）	Not recorded	G7U N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2R)-2-hydroxy-4-oxododecanamido]ethyl}-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；26% PEG 8000, 0.3M sodium acetate, 0.1 M sodium cacodylate pH 6.0,	Resolution 1.93 Å R-free 0.255
9MLW Crosslinked complex of ketosynthase FabB mutant FabBG107M and acyl carrier protein AcpP from E.coli with C8 crosslinker Deposited 2024-12-19	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 2–406（405 aa） Chain B 2–406（405 aa）	Mutation：G107M Mutation：G107M	A1BMZ N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Sodium Cacodylate pH 6.0, 28% PEG8K, NaCH3COO	Resolution 2.21 Å R-free 0.243

16 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FABB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–406； UniProt 1–406 Author chain B； PDBConstruct 1–406； UniProt 1–406 Author chain C； PDBConstruct 1–406； UniProt 1–406 Author chain D； PDBConstruct 1–406； UniProt 1–406

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vb9
Deposition date deposition_date	2007-09-06
Structure title title	beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure
Keywords keywords	FATTY ACID BIOSYNTHESIS, CYTOPLASM, ANTIBIOTIC, TRANSFERASE, ACYLTRANSFERASE, LIPID SYNTHESIS, FATTY ACID SYNTHESIS; 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	39.59 Å
Radius of gyration Rg (electron density) rg_electron	39.50 Å
Forward intensity I(0) i0	455295000.00
Molecular weight molecular_weight	169700.0 kDa
Excluded volume excluded_volume	210090 Å³
Envelope volume envelope_volume	255060 Å³
Hydration-shell volume shell_volume	52954 Å³
Envelope diameter envelope_diameter	126.9 Å
Shell Rg shell_rg	46.07 Å
Envelope Rg envelope_rg	39.13 Å
Shape Rg shape_rg	39.50 Å
Total Rg total_rg	39.82 Å
Total atoms total_atoms	11872
Residues n_residues	1618
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	128.7 Å
Rg (real space) rg_real	39.68 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	4.5530e+08
I(0) uncertainty (real space) i0_real_error	7.5330e+06
Rg (reciprocal space) rg_reciprocal	39.63 Å
I(0) (reciprocal space) i0_reciprocal	455300000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.773
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	219000000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.919

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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 1
Molecular weight formula_weight	42656.2 kDa
EC 编号 ec_number	2.3.1.41
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	14389

MKRAVITGLGIVSSIGNNQQEVLASLREGRSGITFSQELKDSGMRSHVWGNVKLDTTGLIDRKVVRFMSDASIYAFLSMEQAIADAGLSPEAYQNNPRVGLIAGSGGGSPRFQVFGADAMRGPRGLKAVGPYVVTKAMASGVSACLATPFKIHGVNYSISSACATSAHCIGNAVEQIQLGKQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPEKASRTYDAHRDGFVIAGGGGMVVVEELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMKMAMHGVDTPIDYLNSHGTSTPVGDVKELAAIREVFGDKSPAISATKAMTGHSLGAAGVQEAIYSLLMLEHGFIAPSINIEELDEQAAGLNIVTETTDRELTTVMSNSFGFGGTNATLVMRKLKD

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	CHLORIDE ION
Molecular weight formula_weight	35.5 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	2334

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2vb9a1
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	d2vb9a2
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	d2vb9b1
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	d2vb9b2
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	d2vb9c1
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	d2vb9c2
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	d2vb9d1
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	d2vb9d2
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 (8 domains)

Domain ID domain_id	2vb9A01
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	2vb9A02
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	2vb9B01
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	2vb9B02
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	2vb9C01
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	2vb9C02
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	2vb9D01
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	2vb9D02
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

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8. Citations (1)

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Unit-cell length a length_a	58.914 Å
Unit-cell length b length_b	138.355 Å
Unit-cell length c length_c	211.914 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	1.500 Å
Low-resolution limit resolution_low	115.470 Å
R factor r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2380

fit	/app/data/saxs_computation/vb/2vb9/2vb9.fit
pddf	/app/data/pr_computation/vb/2vb9/2vb9.pr.out
profile	/app/data/saxs_computation/vb/2vb9/2vb9.dat