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1bs0

PLP-DEPENDENT ACYL-COA SYNTHASE

Method: X-RAY DIFFRACTION Dmax: 66.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (8-AMINO-7-OXONANOATE 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–384 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–384 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

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 1BS0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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
2G6W Suicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine Deposited 2006-02-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–384（384 aa）
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

3 other PDB entries and 5 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 1bs0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bs0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bs0
Deposition date deposition_date1998-08-31
Structure title titlePLP-DEPENDENT ACYL-COA SYNTHASE
Keywords keywords;PLP-DEPENDENT ACYL-COA SYNTHASE, BIOTIN BIOSYNTHESIS, 8-AMINO-7-OXONANOATE SYNTHASE, 8-AMINO-7-KETOPELARGONATE SYNTHASE, 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_guinier23.01 Å
Radius of gyration Rg (electron density) rg_electron21.78 Å
Forward intensity I(0) i031686300.00
Molecular weight molecular_weight41592.0 kDa
Excluded volume excluded_volume51466 ų
Envelope volume envelope_volume64563 ų
Hydration-shell volume shell_volume24523 ų
Envelope diameter envelope_diameter69.1 Å
Shell Rg shell_rg28.71 Å
Envelope Rg envelope_rg21.80 Å
Shape Rg shape_rg21.79 Å
Total Rg total_rg22.61 Å
Total atoms total_atoms2923
Residues n_residues382
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 dmax66.7 Å
Rg (real space) rg_real22.86 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real3.1690e+07
I(0) uncertainty (real space) i0_real_error3.7250e+05
Rg (reciprocal space) rg_reciprocal22.90 Å
I(0) (reciprocal space) i0_reciprocal31690000.0000
Solution quality estimate total_estimate0.9174
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7 Å
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.639
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5452000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.985; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.975
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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_idd1bs0a_
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_id1bs0A01
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_id1bs0A02
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)