6okf

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16-crypto Acyl Carrier Protein, AcpP

Method: X-RAY DIFFRACTION Dmax: 87.9 Å Quality: EXCELLENT

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

3-oxoacyl-[acyl-carrier-protein] synthase 1

Escherichia coli (strain K12)

UniProt P0A953

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–406 Chain B; UniProt 1–406 Not recorded Acyl carrier protein × 2 (P0A6A8) 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

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.

16 other PDB entries and 28 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

Acyl carrier protein

Escherichia coli (strain K12)

UniProt P0A6A8

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–78 Chain D; UniProt 1–78 Not recorded 3-oxoacyl-[acyl-carrier-protein] synthase 1 × 2 (P0A953) 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

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.

39 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACP_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–78; UniProt 1–78 Author chain D; PDBConstruct 1–78; UniProt 1–78

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

SAXS profile for 6okf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6okf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6okf
Deposition date deposition_date2019-04-12
Structure title titleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16-crypto Acyl Carrier Protein, AcpP
Keywords keywordsThiolase fold, fatty acid synthase, ketosynthase, beta-Ketoacyl-ACP Synthase, KS, AcpP, TRANSFERASE-TRANSPORT PROTEIN complex; TRANSFERASE/TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.78
Radius of gyration Rg (electron density) rg_electron27.83
Forward intensity I(0) i0175011000.00
Molecular weight molecular_weight102490.0 kDa
Excluded volume excluded_volume127140 ų
Envelope volume envelope_volume149360 ų
Hydration-shell volume shell_volume42605 ų
Envelope diameter envelope_diameter91.6
Shell Rg shell_rg36.97
Envelope Rg envelope_rg28.39
Shape Rg shape_rg27.87
Total Rg total_rg28.49
Total atoms total_atoms7176
Residues n_residues962
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.9
Rg (real space) rg_real28.65
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real1.7500e+08
I(0) uncertainty (real space) i0_real_error2.5750e+06
Rg (reciprocal space) rg_reciprocal28.71
I(0) (reciprocal space) i0_reciprocal175000000.0000
Solution quality estimate total_estimate0.9058
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.1
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.511
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51380000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.951

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6okfa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd6okfa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd6okfb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd6okfb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd6okfc_
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.1 — ACP-like
Family Family familya.28.1.1 — Acyl-carrier protein (ACP)
Domain ID domain_idd6okfd_
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.1 — ACP-like
Family Family familya.28.1.1 — Acyl-carrier protein (ACP)

CATH v4.4 (4 domains)

Domain ID domain_id6okfA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id6okfA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id6okfB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id6okfB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase

8. Citations (1)

9. Files and Curves (10)