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2g6w

Suicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine

Method: X-RAY DIFFRACTION Dmax: 67.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

8-amino-7-oxononanoate synthase

Escherichia coli

UniProt P12998

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 1–384 Not recorded LLF (4-{(E)-[(2,2-DIFLUOROETHYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；298 K；0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS, pH 7.0, EVAPORATION, temperature 298K Resolution 2.14 Å R-free 0.246

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 2G6W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BS0 PLP-DEPENDENT ACYL-COA SYNTHASE Deposited 1998-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；PROTEIN WAS CRYSTALLIZED FROM 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS,, pH 7.9
Resolution 1.65 Å R-free 0.212
1BS0 PLP-DEPENDENT ACYL-COA SYNTHASE Deposited 1998-08-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；PROTEIN WAS CRYSTALLIZED FROM 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS,, pH 7.9
Resolution 1.65 Å R-free 0.212
1DJ9 CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY. Deposited 1999-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 KAM N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Resolution 2.00 Å R-free 0.278
1DJ9 CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY. Deposited 1999-12-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 4 MG MAGNESIUM ION × 2 KAM N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Resolution 2.00 Å R-free 0.278
1DJE CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF 8-AMINO-7-OXONANOATE SYNTHASE Deposited 1999-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 3 PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUN CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.71 Å R-free 0.245
1DJE CRYSTAL STRUCTURE OF THE PLP-BOUND FORM OF 8-AMINO-7-OXONANOATE SYNTHASE Deposited 1999-12-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–384（384 aa）
Not recorded SO4 SULFATE ION × 6 PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；AMMONIUM SULPHATE, SODIUN CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.71 Å R-free 0.245

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIOF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–384； UniProt 1–384

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 2g6w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2g6w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2g6w
Deposition date deposition_date2006-02-26
Structure title titleSuicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine
Keywords keywordsbiotin, 8-amino-7-oxonanoate, synthase, PLP, fluoroalanine, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.81 Å
Radius of gyration Rg (electron density) rg_electron21.64 Å
Forward intensity I(0) i031568100.00
Molecular weight molecular_weight41771.0 kDa
Excluded volume excluded_volume51794 ų
Envelope volume envelope_volume63711 ų
Hydration-shell volume shell_volume24330 ų
Envelope diameter envelope_diameter69.2 Å
Shell Rg shell_rg28.61 Å
Envelope Rg envelope_rg21.73 Å
Shape Rg shape_rg21.65 Å
Total Rg total_rg22.46 Å
Total atoms total_atoms2939
Residues n_residues383
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.2 Å
Rg (real space) rg_real22.67 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real3.1570e+07
I(0) uncertainty (real space) i0_real_error3.9560e+05
Rg (reciprocal space) rg_reciprocal22.71 Å
I(0) (reciprocal space) i0_reciprocal31570000.0000
Solution quality estimate total_estimate0.9164
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.089
Kurtosis Kurtosis kurtosis-0.637
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5387000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.981
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2g6wa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id2g6wA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id2g6wA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
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8. Citations (1)

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9. Files and Curves (10)