2gyo

Methanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synthase III (FabH) and Coenzyme A

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: GOOD

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

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

Escherichia coli

UniProt P0A6R0

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 1–317 Chain B; UniProt 1–317 Not recorded COA COENZYME A × 1 MEE METHANETHIOL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;295 K;1.7M ammonium sulfate, 2% PEG400, 100 mM Na Hepes (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.00 Å R-free 0.268

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.

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FABH_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–317; UniProt 1–317 Author chain B; PDBConstruct 1–317; UniProt 1–317

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 2gyo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gyo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gyo
Deposition date deposition_date2006-05-09
Structure title titleMethanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synthase III (FabH) and Coenzyme A
Keywords keywordsfatty acid biosynthesis, alkyl-coa-disulfide, mechanism-based inhibitor, mycobacterium tuberculosis, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.14
Radius of gyration Rg (electron density) rg_electron23.94
Forward intensity I(0) i077629700.00
Molecular weight molecular_weight67578.0 kDa
Excluded volume excluded_volume83987 ų
Envelope volume envelope_volume95621 ų
Hydration-shell volume shell_volume32256 ų
Envelope diameter envelope_diameter81.9
Shell Rg shell_rg32.23
Envelope Rg envelope_rg24.18
Shape Rg shape_rg23.92
Total Rg total_rg24.82
Total atoms total_atoms4732
Residues n_residues634
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 dmax79.2
Rg (real space) rg_real25.05
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real7.7630e+07
I(0) uncertainty (real space) i0_real_error9.9530e+05
Rg (reciprocal space) rg_reciprocal25.08
I(0) (reciprocal space) i0_reciprocal77630000.0000
Solution quality estimate total_estimate0.8981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.2
Skewness Skewness skewness0.275
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19960000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2gyoa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd2gyoa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd2gyob1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd2gyob2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like

CATH v4.4 (4 domains)

Domain ID domain_id2gyoA01
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_id2gyoA02
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_id2gyoB01
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_id2gyoB02
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)